diff --git a/Cargo.lock b/Cargo.lock
index cabb1cad..b752b267 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -410,6 +410,7 @@ dependencies = [
 name = "configuration"
 version = "0.1.0"
 dependencies = [
+ "anyhow",
  "futures",
  "itertools 0.12.1",
  "mongodb",
diff --git a/crates/cli/src/lib.rs b/crates/cli/src/lib.rs
index e06babca..4843459b 100644
--- a/crates/cli/src/lib.rs
+++ b/crates/cli/src/lib.rs
@@ -43,7 +43,7 @@ async fn update(context: &Context, args: &UpdateArgs) -> anyhow::Result<()> {
             introspection::sample_schema_from_db(sample_size, &context.mongo_config).await?
         }
     };
-    let configuration = Configuration::from_schema(schema);
+    let configuration = Configuration::from_schema(schema)?;
 
     configuration::write_directory(&context.path, &configuration).await?;
 
diff --git a/crates/configuration/Cargo.toml b/crates/configuration/Cargo.toml
index bea1d0e8..8db65e2e 100644
--- a/crates/configuration/Cargo.toml
+++ b/crates/configuration/Cargo.toml
@@ -4,6 +4,7 @@ version = "0.1.0"
 edition = "2021"
 
 [dependencies]
+anyhow = "1"
 futures = "^0.3"
 itertools = "^0.12"
 mongodb = "2.8"
diff --git a/crates/configuration/src/configuration.rs b/crates/configuration/src/configuration.rs
index 3a3549f9..8a5bd1a6 100644
--- a/crates/configuration/src/configuration.rs
+++ b/crates/configuration/src/configuration.rs
@@ -1,9 +1,11 @@
-use std::{io, path::Path};
+use std::path::Path;
 
+use anyhow::ensure;
+use itertools::Itertools;
 use schemars::JsonSchema;
 use serde::Deserialize;
 
-use crate::{native_queries::NativeQuery, read_directory, Schema};
+use crate::{native_queries::NativeQuery, read_directory, schema::ObjectType, Schema};
 
 #[derive(Clone, Debug, Default, Deserialize, JsonSchema)]
 #[serde(rename_all = "camelCase")]
@@ -18,16 +20,98 @@ pub struct Configuration {
 }
 
 impl Configuration {
-    pub fn from_schema(schema: Schema) -> Self {
-        Self {
+    pub fn validate(schema: Schema, native_queries: Vec<NativeQuery>) -> anyhow::Result<Self> {
+        let config = Configuration {
             schema,
-            ..Default::default()
+            native_queries,
+        };
+
+        {
+            let duplicate_type_names: Vec<&str> = config
+                .object_types()
+                .map(|t| t.name.as_ref())
+                .duplicates()
+                .collect();
+            ensure!(
+                duplicate_type_names.is_empty(),
+                "configuration contains multiple definitions for these object type names: {}",
+                duplicate_type_names.join(", ")
+            );
+        }
+
+        {
+            let duplicate_collection_names: Vec<&str> = config
+                .schema
+                .collections
+                .iter()
+                .map(|c| c.name.as_ref())
+                .duplicates()
+                .collect();
+            ensure!(
+                duplicate_collection_names.is_empty(),
+                "configuration contains multiple definitions for these collection names: {}",
+                duplicate_collection_names.join(", ")
+            );
         }
+
+        Ok(config)
+    }
+
+    pub fn from_schema(schema: Schema) -> anyhow::Result<Self> {
+        Self::validate(schema, Default::default())
     }
 
     pub async fn parse_configuration(
         configuration_dir: impl AsRef<Path> + Send,
-    ) -> io::Result<Self> {
+    ) -> anyhow::Result<Self> {
         read_directory(configuration_dir).await
     }
+
+    /// Returns object types collected from schema and native queries
+    pub fn object_types(&self) -> impl Iterator<Item = &ObjectType> {
+        let object_types_from_schema = self.schema.object_types.iter();
+        let object_types_from_native_queries = self
+            .native_queries
+            .iter()
+            .flat_map(|native_query| &native_query.object_types);
+        object_types_from_schema.chain(object_types_from_native_queries)
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use mongodb::bson::doc;
+
+    use super::*;
+    use crate::{schema::Type, Schema};
+
+    #[test]
+    fn fails_with_duplicate_object_types() {
+        let schema = Schema {
+            collections: Default::default(),
+            object_types: vec![ObjectType {
+                name: "Album".to_owned(),
+                fields: Default::default(),
+                description: Default::default(),
+            }],
+        };
+        let native_queries = vec![NativeQuery {
+            name: "hello".to_owned(),
+            object_types: vec![ObjectType {
+                name: "Album".to_owned(),
+                fields: Default::default(),
+                description: Default::default(),
+            }],
+            result_type: Type::Object("Album".to_owned()),
+            command: doc! { "command": 1 },
+            arguments: Default::default(),
+            selection_criteria: Default::default(),
+            description: Default::default(),
+            mode: Default::default(),
+        }];
+        let result = Configuration::validate(schema, native_queries);
+        let error_msg = result.unwrap_err().to_string();
+        assert!(error_msg.contains("multiple definitions"));
+        assert!(error_msg.contains("Album"));
+    }
 }
diff --git a/crates/configuration/src/directory.rs b/crates/configuration/src/directory.rs
index f80d4b23..fd616e71 100644
--- a/crates/configuration/src/directory.rs
+++ b/crates/configuration/src/directory.rs
@@ -1,10 +1,8 @@
+use anyhow::{anyhow, Context as _};
 use futures::stream::TryStreamExt as _;
 use itertools::Itertools as _;
 use serde::{Deserialize, Serialize};
-use std::{
-    io,
-    path::{Path, PathBuf},
-};
+use std::path::{Path, PathBuf};
 use tokio::fs;
 use tokio_stream::wrappers::ReadDirStream;
 
@@ -29,7 +27,7 @@ const YAML: FileFormat = FileFormat::Yaml;
 /// Read configuration from a directory
 pub async fn read_directory(
     configuration_dir: impl AsRef<Path> + Send,
-) -> io::Result<Configuration> {
+) -> anyhow::Result<Configuration> {
     let dir = configuration_dir.as_ref();
 
     let schema = parse_json_or_yaml(dir, SCHEMA_FILENAME).await?;
@@ -38,16 +36,13 @@ pub async fn read_directory(
         .await?
         .unwrap_or_default();
 
-    Ok(Configuration {
-        schema,
-        native_queries,
-    })
+    Configuration::validate(schema, native_queries)
 }
 
 /// Parse all files in a directory with one of the allowed configuration extensions according to
 /// the given type argument. For example if `T` is `NativeQuery` this function assumes that all
 /// json and yaml files in the given directory should be parsed as native query configurations.
-async fn read_subdir_configs<T>(subdir: &Path) -> io::Result<Option<Vec<T>>>
+async fn read_subdir_configs<T>(subdir: &Path) -> anyhow::Result<Option<Vec<T>>>
 where
     for<'a> T: Deserialize<'a>,
 {
@@ -57,6 +52,7 @@ where
 
     let dir_stream = ReadDirStream::new(fs::read_dir(subdir).await?);
     let configs = dir_stream
+        .map_err(|err| err.into())
         .try_filter_map(|dir_entry| async move {
             // Permits regular files and symlinks, does not filter out symlinks to directories.
             let is_file = !(dir_entry.file_type().await?.is_dir());
@@ -86,7 +82,7 @@ where
 
 /// Given a base name, like "connection", looks for files of the form "connection.json",
 /// "connection.yaml", etc; reads the file; and parses it according to its extension.
-async fn parse_json_or_yaml<T>(configuration_dir: &Path, basename: &str) -> io::Result<T>
+async fn parse_json_or_yaml<T>(configuration_dir: &Path, basename: &str) -> anyhow::Result<T>
 where
     for<'a> T: Deserialize<'a>,
 {
@@ -96,7 +92,10 @@ where
 
 /// Given a base name, like "connection", looks for files of the form "connection.json",
 /// "connection.yaml", etc, and returns the found path with its file format.
-async fn find_file(configuration_dir: &Path, basename: &str) -> io::Result<(PathBuf, FileFormat)> {
+async fn find_file(
+    configuration_dir: &Path,
+    basename: &str,
+) -> anyhow::Result<(PathBuf, FileFormat)> {
     for (extension, format) in CONFIGURATION_EXTENSIONS {
         let path = configuration_dir.join(format!("{basename}.{extension}"));
         if fs::try_exists(&path).await? {
@@ -104,30 +103,28 @@ async fn find_file(configuration_dir: &Path, basename: &str) -> io::Result<(Path
         }
     }
 
-    Err(io::Error::new(
-        io::ErrorKind::NotFound,
-        format!(
-            "could not find file, {:?}",
-            configuration_dir.join(format!(
-                "{basename}.{{{}}}",
-                CONFIGURATION_EXTENSIONS
-                    .into_iter()
-                    .map(|(ext, _)| ext)
-                    .join(",")
-            ))
-        ),
+    Err(anyhow!(
+        "could not find file, {:?}",
+        configuration_dir.join(format!(
+            "{basename}.{{{}}}",
+            CONFIGURATION_EXTENSIONS
+                .into_iter()
+                .map(|(ext, _)| ext)
+                .join(",")
+        ))
     ))
 }
 
-async fn parse_config_file<T>(path: impl AsRef<Path>, format: FileFormat) -> io::Result<T>
+async fn parse_config_file<T>(path: impl AsRef<Path>, format: FileFormat) -> anyhow::Result<T>
 where
     for<'a> T: Deserialize<'a>,
 {
     let bytes = fs::read(path.as_ref()).await?;
     let value = match format {
-        FileFormat::Json => serde_json::from_slice(&bytes)?,
+        FileFormat::Json => serde_json::from_slice(&bytes)
+            .with_context(|| format!("error parsing {:?}", path.as_ref()))?,
         FileFormat::Yaml => serde_yaml::from_slice(&bytes)
-            .map_err(|err| io::Error::new(io::ErrorKind::Other, err))?,
+            .with_context(|| format!("error parsing {:?}", path.as_ref()))?,
     };
     Ok(value)
 }
@@ -136,7 +133,7 @@ where
 pub async fn write_directory(
     configuration_dir: impl AsRef<Path>,
     configuration: &Configuration,
-) -> io::Result<()> {
+) -> anyhow::Result<()> {
     write_file(configuration_dir, SCHEMA_FILENAME, &configuration.schema).await
 }
 
@@ -149,11 +146,13 @@ async fn write_file<T>(
     configuration_dir: impl AsRef<Path>,
     basename: &str,
     value: &T,
-) -> io::Result<()>
+) -> anyhow::Result<()>
 where
     T: Serialize,
 {
     let path = default_file_path(configuration_dir, basename);
     let bytes = serde_json::to_vec_pretty(value)?;
-    fs::write(path, bytes).await
+    fs::write(path.clone(), bytes)
+        .await
+        .with_context(|| format!("error writing {:?}", path))
 }
diff --git a/crates/configuration/src/native_queries.rs b/crates/configuration/src/native_queries.rs
index 633c9ead..6153a4bf 100644
--- a/crates/configuration/src/native_queries.rs
+++ b/crates/configuration/src/native_queries.rs
@@ -2,7 +2,7 @@ use mongodb::{bson, options::SelectionCriteria};
 use schemars::JsonSchema;
 use serde::Deserialize;
 
-use crate::schema::{ObjectField, Type};
+use crate::schema::{ObjectField, ObjectType, Type};
 
 /// An arbitrary database command using MongoDB's runCommand API.
 /// See https://www.mongodb.com/docs/manual/reference/method/db.runCommand/
@@ -12,10 +12,19 @@ pub struct NativeQuery {
     /// Name that will be used to identify the query in your data graph
     pub name: String,
 
-    /// Type of data returned by the query.
+    /// You may define object types here to reference in `result_type`. Any types defined here will
+    /// be merged with the definitions in `schema.json`. This allows you to maintain hand-written
+    /// types for native queries without having to edit a generated `schema.json` file.
+    #[serde(default, skip_serializing_if = "Vec::is_empty")]
+    pub object_types: Vec<ObjectType>,
+
+    /// Type of data returned by the query. You may reference object types defined in the
+    /// `object_types` list in this definition, or you may reference object types from
+    /// `schema.json`.
     pub result_type: Type,
 
     /// Arguments for per-query customization
+    #[serde(default)]
     pub arguments: Vec<ObjectField>,
 
     /// Command to run expressed as a BSON document
@@ -31,7 +40,11 @@ pub struct NativeQuery {
     #[serde(default, skip_serializing_if = "Option::is_none")]
     pub description: Option<String>,
 
-    /// Set to `readWrite` if this native query might modify data in the database.
+    /// Set to `readWrite` if this native query might modify data in the database. When refreshing
+    /// a dataconnector native queries will appear in the corresponding `DataConnectorLink`
+    /// definition as `functions` if they are read-only, or as `procedures` if they are read-write.
+    /// Functions are intended to map to GraphQL Query fields, while procedures map to Mutation
+    /// fields.
     #[serde(default)]
     pub mode: Mode,
 }
diff --git a/crates/mongodb-agent-common/src/query/execute_native_query_request.rs b/crates/mongodb-agent-common/src/query/execute_native_query_request.rs
new file mode 100644
index 00000000..ff603dd0
--- /dev/null
+++ b/crates/mongodb-agent-common/src/query/execute_native_query_request.rs
@@ -0,0 +1,31 @@
+use configuration::native_queries::NativeQuery;
+use dc_api::JsonResponse;
+use dc_api_types::{QueryResponse, ResponseFieldValue, RowSet};
+use mongodb::Database;
+
+use crate::interface_types::MongoAgentError;
+
+pub async fn handle_native_query_request(
+    native_query: NativeQuery,
+    database: Database,
+) -> Result<JsonResponse<QueryResponse>, MongoAgentError> {
+    let result = database
+        .run_command(native_query.command, native_query.selection_criteria)
+        .await?;
+    let result_json =
+        serde_json::to_value(result).map_err(|err| MongoAgentError::AdHoc(err.into()))?;
+
+    // A function returs a single row with a single column called `__value`
+    // https://hasura.github.io/ndc-spec/specification/queries/functions.html
+    let response_row = [(
+        "__value".to_owned(),
+        ResponseFieldValue::Column(result_json),
+    )]
+    .into_iter()
+    .collect();
+
+    Ok(JsonResponse::Value(QueryResponse::Single(RowSet {
+        aggregates: None,
+        rows: Some(vec![response_row]),
+    })))
+}
diff --git a/crates/mongodb-agent-common/src/query/mod.rs b/crates/mongodb-agent-common/src/query/mod.rs
index ed0abc68..5f32bee9 100644
--- a/crates/mongodb-agent-common/src/query/mod.rs
+++ b/crates/mongodb-agent-common/src/query/mod.rs
@@ -1,5 +1,6 @@
 mod column_ref;
 mod constants;
+mod execute_native_query_request;
 mod execute_query_request;
 mod foreach;
 mod make_selector;
@@ -17,7 +18,10 @@ pub use self::{
     make_sort::make_sort,
     pipeline::{is_response_faceted, pipeline_for_non_foreach, pipeline_for_query_request},
 };
-use crate::interface_types::{MongoAgentError, MongoConfig};
+use crate::{
+    interface_types::{MongoAgentError, MongoConfig},
+    query::execute_native_query_request::handle_native_query_request,
+};
 
 pub fn collection_name(query_request_target: &Target) -> String {
     query_request_target.name().join(".")
@@ -29,10 +33,17 @@ pub async fn handle_query_request(
 ) -> Result<JsonResponse<QueryResponse>, MongoAgentError> {
     tracing::debug!(?config, query_request = %serde_json::to_string(&query_request).unwrap(), "executing query");
 
-    let collection = config
-        .client
-        .database(&config.database)
-        .collection::<Document>(&collection_name(&query_request.target));
+    let database = config.client.database(&config.database);
+
+    let target = &query_request.target;
+    if let Some(native_query) = config.native_queries.iter().find(|query| {
+        let target_name = target.name();
+        target_name.len() == 1 && target_name[0] == query.name
+    }) {
+        return handle_native_query_request(native_query.clone(), database).await;
+    }
+
+    let collection = database.collection::<Document>(&collection_name(&query_request.target));
 
     execute_query_request(&collection, query_request).await
 }
diff --git a/crates/mongodb-connector/src/mongo_connector.rs b/crates/mongodb-connector/src/mongo_connector.rs
index e7e18b2d..f23c4338 100644
--- a/crates/mongodb-connector/src/mongo_connector.rs
+++ b/crates/mongodb-connector/src/mongo_connector.rs
@@ -39,7 +39,9 @@ impl Connector for MongoConnector {
     async fn parse_configuration(
         configuration_dir: impl AsRef<Path> + Send,
     ) -> Result<Self::Configuration, ParseError> {
-        let configuration = Configuration::parse_configuration(configuration_dir).await?;
+        let configuration = Configuration::parse_configuration(configuration_dir)
+            .await
+            .map_err(|err| ParseError::Other(err.into()))?;
         Ok(configuration)
     }
 
diff --git a/crates/mongodb-connector/src/schema.rs b/crates/mongodb-connector/src/schema.rs
index 5cb4a7a5..d5f265e8 100644
--- a/crates/mongodb-connector/src/schema.rs
+++ b/crates/mongodb-connector/src/schema.rs
@@ -12,8 +12,8 @@ pub async fn get_schema(
     config: &Configuration,
 ) -> Result<models::SchemaResponse, connector::SchemaError> {
     let schema = &config.schema;
-    let object_types = map_object_types(&schema.object_types);
     let collections = schema.collections.iter().map(map_collection).collect();
+    let object_types = config.object_types().map(map_object_type).collect();
 
     let functions = config
         .native_queries
@@ -38,19 +38,14 @@ pub async fn get_schema(
     })
 }
 
-fn map_object_types(object_types: &[schema::ObjectType]) -> BTreeMap<String, models::ObjectType> {
-    object_types
-        .iter()
-        .map(|t| {
-            (
-                t.name.clone(),
-                models::ObjectType {
-                    fields: map_field_infos(&t.fields),
-                    description: t.description.clone(),
-                },
-            )
-        })
-        .collect()
+fn map_object_type(object_type: &schema::ObjectType) -> (String, models::ObjectType) {
+    (
+        object_type.name.clone(),
+        models::ObjectType {
+            fields: map_field_infos(&object_type.fields),
+            description: object_type.description.clone(),
+        },
+    )
 }
 
 fn map_field_infos(fields: &[schema::ObjectField]) -> BTreeMap<String, models::ObjectField> {
diff --git a/fixtures/connector/chinook/native_queries/hello.yaml b/fixtures/connector/chinook/native_queries/hello.yaml
new file mode 100644
index 00000000..36b14855
--- /dev/null
+++ b/fixtures/connector/chinook/native_queries/hello.yaml
@@ -0,0 +1,12 @@
+name: hello
+objectTypes:
+  - name: HelloResult
+    fields:
+      - name: ok
+        type: !scalar int
+      - name: readOnly
+        type: !scalar bool
+      # There are more fields but you get the idea
+resultType: !object HelloResult
+command:
+  hello: 1
diff --git a/fixtures/connector/chinook/schema.json b/fixtures/connector/chinook/schema.json
new file mode 100644
index 00000000..4c7ee983
--- /dev/null
+++ b/fixtures/connector/chinook/schema.json
@@ -0,0 +1,742 @@
+{
+  "collections": [
+    {
+      "name": "Invoice",
+      "type": "Invoice",
+      "description": null
+    },
+    {
+      "name": "Track",
+      "type": "Track",
+      "description": null
+    },
+    {
+      "name": "MediaType",
+      "type": "MediaType",
+      "description": null
+    },
+    {
+      "name": "InvoiceLine",
+      "type": "InvoiceLine",
+      "description": null
+    },
+    {
+      "name": "Employee",
+      "type": "Employee",
+      "description": null
+    },
+    {
+      "name": "PlaylistTrack",
+      "type": "PlaylistTrack",
+      "description": null
+    },
+    {
+      "name": "Album",
+      "type": "Album",
+      "description": null
+    },
+    {
+      "name": "Genre",
+      "type": "Genre",
+      "description": null
+    },
+    {
+      "name": "Artist",
+      "type": "Artist",
+      "description": null
+    },
+    {
+      "name": "Playlist",
+      "type": "Playlist",
+      "description": null
+    },
+    {
+      "name": "Customer",
+      "type": "Customer",
+      "description": null
+    }
+  ],
+  "objectTypes": [
+    {
+      "name": "Invoice",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "BillingAddress",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "BillingCity",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "BillingCountry",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "BillingPostalCode",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "BillingState",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "CustomerId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "InvoiceDate",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        },
+        {
+          "name": "InvoiceId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Total",
+          "type": {
+            "scalar": "double"
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Invoice"
+    },
+    {
+      "name": "Track",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "AlbumId",
+          "type": {
+            "nullable": {
+              "scalar": "int"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Bytes",
+          "type": {
+            "nullable": {
+              "scalar": "int"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Composer",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "GenreId",
+          "type": {
+            "nullable": {
+              "scalar": "int"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "MediaTypeId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Milliseconds",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Name",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        },
+        {
+          "name": "TrackId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "UnitPrice",
+          "type": {
+            "scalar": "double"
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Track"
+    },
+    {
+      "name": "MediaType",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "MediaTypeId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Name",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection MediaType"
+    },
+    {
+      "name": "InvoiceLine",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "InvoiceId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "InvoiceLineId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Quantity",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "TrackId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "UnitPrice",
+          "type": {
+            "scalar": "double"
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection InvoiceLine"
+    },
+    {
+      "name": "Employee",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Address",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "BirthDate",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "City",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Country",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Email",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "EmployeeId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Fax",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "FirstName",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        },
+        {
+          "name": "HireDate",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "LastName",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        },
+        {
+          "name": "Phone",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "PostalCode",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "ReportsTo",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "State",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Title",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Employee"
+    },
+    {
+      "name": "PlaylistTrack",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "PlaylistId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "TrackId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection PlaylistTrack"
+    },
+    {
+      "name": "Album",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "AlbumId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "ArtistId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Title",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Album"
+    },
+    {
+      "name": "Genre",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "GenreId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Name",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Genre"
+    },
+    {
+      "name": "Artist",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "ArtistId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Name",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Artist"
+    },
+    {
+      "name": "Playlist",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Name",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "PlaylistId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Playlist"
+    },
+    {
+      "name": "Customer",
+      "fields": [
+        {
+          "name": "_id",
+          "type": {
+            "nullable": {
+              "scalar": "objectId"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Address",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "City",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Company",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "Country",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "CustomerId",
+          "type": {
+            "scalar": "int"
+          },
+          "description": null
+        },
+        {
+          "name": "Email",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        },
+        {
+          "name": "Fax",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "FirstName",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        },
+        {
+          "name": "LastName",
+          "type": {
+            "scalar": "string"
+          },
+          "description": null
+        },
+        {
+          "name": "Phone",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "PostalCode",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "State",
+          "type": {
+            "nullable": {
+              "scalar": "string"
+            }
+          },
+          "description": null
+        },
+        {
+          "name": "SupportRepId",
+          "type": {
+            "nullable": {
+              "scalar": "int"
+            }
+          },
+          "description": null
+        }
+      ],
+      "description": "Object type for collection Customer"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/fixtures/connector/chinook/schema.yaml b/fixtures/connector/chinook/schema.yaml
deleted file mode 100644
index bbb4a52c..00000000
--- a/fixtures/connector/chinook/schema.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-collections:
-  - name: Album
-    type: Album
-
-objectTypes:
-  - name: Album
-    fields:
-      - name: _id
-        type: !scalar objectId
-      - name: AlbumId
-        type: !scalar int
-      - name: ArtistId
-        type: !scalar int
-      - name: Title
-        type: !scalar string
diff --git a/fixtures/ddn/subgraphs/chinook/commands/Hello.hml b/fixtures/ddn/subgraphs/chinook/commands/Hello.hml
new file mode 100644
index 00000000..cfdebd65
--- /dev/null
+++ b/fixtures/ddn/subgraphs/chinook/commands/Hello.hml
@@ -0,0 +1,53 @@
+kind: Command
+version: v1
+definition:
+  name: hello
+  description: Example of a read-only native query
+  outputType: HelloResult
+  arguments: []
+  source:
+    dataConnectorName: mongodb
+    dataConnectorCommand:
+      function: hello
+    typeMapping:
+      HelloResult:
+        fieldMapping:
+          ok: { column: ok }
+          readOnly: { column: readOnly }
+  graphql:
+    rootFieldName: hello
+    rootFieldKind: Query
+
+---
+kind: CommandPermissions
+version: v1
+definition:
+  commandName: hello
+  permissions:
+    - role: admin
+      allowExecution: true
+    
+---
+kind: ObjectType
+version: v1
+definition:
+  name: HelloResult
+  graphql:
+    typeName: HelloResult
+  fields:
+    - name: ok
+      type: Int!
+    - name: readOnly
+      type: Boolean!
+
+---
+kind: TypePermissions
+version: v1
+definition:
+  typeName: HelloResult
+  permissions:
+    - role: admin
+      output:
+        allowedFields:
+          - ok
+          - readOnly
diff --git a/fixtures/ddn/subgraphs/chinook/dataconnectors/mongodb.hml b/fixtures/ddn/subgraphs/chinook/dataconnectors/mongodb.hml
index 4167b898..4eb5585b 100644
--- a/fixtures/ddn/subgraphs/chinook/dataconnectors/mongodb.hml
+++ b/fixtures/ddn/subgraphs/chinook/dataconnectors/mongodb.hml
@@ -905,6 +905,12 @@ definition:
                 underlying_type:
                   type: named
                   name: ObjectId
+        HelloResult:
+          fields:
+            ok:
+              type: { type: named, name: Int }
+            readOnly:
+              type: { type: named, name: Boolean }
       collections:
         - name: Album
           arguments: {}
@@ -994,7 +1000,11 @@ definition:
               unique_columns:
                 - _id
           foreign_keys: {}
-      functions: []
+      functions:
+        - name: hello
+          result_type: { type: named, name: HelloResult } 
+          arguments: {}
+          command: { hello: 1 }
       procedures: []
     capabilities:
       version: ^0.1.0