Merge pull request #16 from FAIRChemistry/dataset-validation

JSON Dataset validation

Cargo.toml

@@ -33,6 +33,7 @@ wasm-bindgen = { version = "0.2.95", optional = true }
 serde-wasm-bindgen = { version = "0.6.5", optional = true }
 tokio = { version = "1.42.0", features = ["rt"] }
 openai-api-rs = { version = "5.2.3", optional = true }
+jsonschema = { version = "0.26.2", default-features = false }
 
 [features]
 default = ["openai"]

src/bin/cli.rs

@@ -23,9 +23,11 @@
 
 use clap::{Parser, Subcommand};
 use colored::Colorize;
+use log::error;
 use mdmodels::{
     datamodel::DataModel,
     exporters::{render_jinja_template, Templates},
+    json::validation::validate_json,
     llm::extraction::query_openai,
     pipeline::process_pipeline,
 };
@@ -53,6 +55,8 @@ enum Commands {
     Pipeline(PipelineArgs),
     /// Large Language Model Extraction
     Extract(ExtractArgs),
+    /// Validate a dataset against a markdown model.
+    Dataset(DatasetArgs),
 }
 
 /// Arguments for the validate subcommand.
@@ -141,6 +145,33 @@ struct ExtractArgs {
     multiple: bool,
 }
 
+/// Arguments for the dataset subcommand.
+#[derive(Parser, Debug)]
+struct DatasetArgs {
+    #[command(subcommand)]
+    command: DatasetCommands,
+}
+
+/// Subcommands for dataset operations
+#[derive(Subcommand, Debug)]
+enum DatasetCommands {
+    /// Validate a dataset against a markdown model.
+    Validate(ValidateDatasetArgs),
+    // Add more dataset subcommands here as needed
+}
+
+/// Arguments for the validate dataset subcommand.
+#[derive(Parser, Debug)]
+struct ValidateDatasetArgs {
+    /// Path to the dataset file.
+    #[arg(short, long, help = "Path to the dataset file")]
+    input: InputType,
+
+    /// Path to the markdown model.
+    #[arg(short, long, help = "Path to the markdown model")]
+    model: InputType,
+}
+
 /// Represents the input type, either remote URL or local file path.
 #[derive(Deserialize, Serialize, Clone, Debug)]
 enum InputType {
@@ -186,6 +217,9 @@ fn main() -> Result<(), Box<dyn Error>> {
         Commands::Convert(args) => convert(args),
         Commands::Pipeline(args) => process_pipeline(&args.input),
         Commands::Extract(args) => query_llm(args),
+        Commands::Dataset(args) => match args.command {
+            DatasetCommands::Validate(args) => validate_ds(args),
+        },
     }
 }
 
@@ -355,6 +389,20 @@ fn render_all_json_schemes(
     Ok(())
 }
 
+/// Validates a dataset against a markdown model.
+fn validate_ds(args: ValidateDatasetArgs) -> Result<(), Box<dyn Error>> {
+    let model_path = resolve_input_path(&args.model);
+    let model = DataModel::from_markdown(&model_path)?;
+    let dataset_path = resolve_input_path(&args.input);
+    let result = validate_json(dataset_path, &model, None)?;
+
+    for error in result {
+        error!("{}", error);
+    }
+
+    Ok(())
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;

src/bindings/python.rs

@@ -82,7 +82,7 @@ impl DataModel {
     ///
     /// A string that represents the `DataModel` instance.
     fn __repr__(&self) -> String {
-        self.model.sdrdm_schema()
+        self.model.internal_schema()
     }
 
     /// Converts the `DataModel` instance to a specified template format.

src/datamodel.rs

@@ -30,6 +30,7 @@ use serde::{Deserialize, Serialize};
 
 use crate::exporters::{render_jinja_template, Templates};
 use crate::json::export::to_json_schema;
+use crate::json::validation::{validate_json, ValidationError};
 use crate::markdown::frontmatter::FrontMatter;
 use crate::markdown::parser::parse_markdown;
 use crate::object::{Enumeration, Object};
@@ -60,7 +61,7 @@ use pyo3::pyclass;
 // * `parse` - Parse a markdown file and create a data model
 // * `json_schema` - Generate a JSON schema from the data model
 // * `json_schema_all` - Generate JSON schemas for all objects in the data model
-// * `sdrdm_schema` - Generate a SDRDM schema from the data model
+// * `internal_schema` - Generate an internal schema from the data model
 #[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
 #[cfg_attr(feature = "python", pyclass(get_all))]
 pub struct DataModel {
@@ -82,6 +83,28 @@ impl DataModel {
         }
     }
 
+    /// Validates a dataset against the data model.
+    ///
+    /// This function takes the path to a dataset and validates it against the
+    /// current data model. It returns a vector of validation errors if any
+    /// validation issues are found, or an empty vector if the validation is successful.
+    ///
+    /// # Arguments
+    ///
+    /// * `path` - A reference to the path of the dataset to validate.
+    /// * `root` - An optional root path for the schema. Will use the first object if not provided.
+    ///
+    /// # Returns
+    /// A Result containing a vector of `ValidationError` if validation fails,
+    /// or an empty vector if successful.
+    pub fn validate_json(
+        &self,
+        path: &Path,
+        root: Option<String>,
+    ) -> Result<Vec<ValidationError>, Box<dyn Error>> {
+        validate_json(path.to_path_buf(), self, root)
+    }
+
     // Get the JSON schema for an object
     //
     // * `obj_name` - Name of the object
@@ -166,7 +189,7 @@ impl DataModel {
         Ok(())
     }
 
-    // Get the SDRDM schema for the markdown file
+    // Get the internal schema for the markdown file
     //
     // # Panics
     //
@@ -177,18 +200,18 @@ impl DataModel {
     // ```
     // let model = DataModel::new();
     // model.parse("path/to/file.md".to_string());
-    // let schema = model.sdrdm_schema();
+    // let schema = model.internal_schema();
     // ```
     //
     // # Returns
     //
-    // A SDRDM schema string
-    pub fn sdrdm_schema(&self) -> String {
+    // An internal schema string
+    pub fn internal_schema(&self) -> String {
         if self.objects.is_empty() {
             panic!("No objects found in the markdown file");
         }
 
-        serde_json::to_string_pretty(&self).expect("Could not serialize to sdRDM schema")
+        serde_json::to_string_pretty(&self).expect("Could not serialize to internal schema")
     }
 
     // Parse a markdown file and create a data model
@@ -199,14 +222,14 @@ impl DataModel {
     //
     // ```
     // let path = Path::new("path/to/file.md");
-    // let model = DataModel::from_sdrdm_schema(path);
+    // let model = DataModel::from_internal_schema(path);
     // ```
     //
     // # Returns
     //
     // A data model
     //
-    pub fn from_sdrdm_schema(path: &Path) -> Result<Self, Box<dyn Error>> {
+    pub fn from_internal_schema(path: &Path) -> Result<Self, Box<dyn Error>> {
         if !path.exists() {
             return Err("File does not exist".into());
         }
@@ -457,12 +480,12 @@ mod tests {
     }
 
     #[test]
-    fn test_from_sdrdm_schema() {
+    fn test_from_internal_schema() {
         // Arrange
-        let path = Path::new("tests/data/expected_sdrdm_schema.json");
+        let path = Path::new("tests/data/expected_internal_schema.json");
 
         // Act
-        let model = DataModel::from_sdrdm_schema(path).expect("Failed to parse SDRDM schema");
+        let model = DataModel::from_internal_schema(path).expect("Failed to parse internal schema");
 
         // Assert
         assert_eq!(model.objects.len(), 2);

src/json/validation.rs

@@ -0,0 +1,151 @@
+/*
+ * Copyright (c) 2024 Jan Range
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ */
+
+use std::error::Error;
+use std::path::PathBuf;
+
+use colored::Colorize;
+use jsonschema::error::ValidationErrorKind;
+use serde_json::Value;
+use std::convert::TryFrom;
+
+use crate::datamodel::DataModel;
+use jsonschema::validator_for;
+
+/// Represents a validation error that occurs during dataset validation.
+#[derive(Debug)]
+pub struct ValidationError {
+    pub instance_path: String,
+    pub schema_path: String,
+    pub message: String,
+    pub kind: ValidationErrorKind,
+}
+
+impl std::fmt::Display for ValidationError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        write!(
+            f,
+            "Validation Error: Instance {} violates schema at {}: {}",
+            self.instance_path.red().bold(),
+            self.schema_path.green().bold(),
+            self.message.yellow().bold()
+        )
+    }
+}
+
+impl From<jsonschema::ValidationError<'_>> for ValidationError {
+    fn from(err: jsonschema::ValidationError) -> Self {
+        ValidationError {
+            instance_path: err.instance_path.to_string(),
+            schema_path: err.schema_path.to_string(),
+            message: err.to_string(),
+            kind: err.kind,
+        }
+    }
+}
+
+/// Validates a dataset against a given DataModel.
+///
+/// # Arguments
+///
+/// * `dataset` - The dataset to validate, which can be provided in various forms.
+/// * `model` - A reference to the DataModel against which the dataset will be validated.
+/// * `root` - An optional root path for the schema.
+///
+/// # Returns
+///
+/// A Result containing a vector of ValidationErrors if validation fails, or an empty vector if successful.
+pub fn validate_json<T: Into<DatasetInput>>(
+    dataset: T,
+    model: &DataModel,
+    root: Option<String>,
+) -> Result<Vec<ValidationError>, Box<dyn Error>> {
+    // Convert the dataset input to a Value
+    let dataset_input: DatasetInput = dataset.into();
+    let value: Value = dataset_input.try_into()?;
+
+    // Get the JSON Schema from the model
+    let schema = model.json_schema(root, false)?;
+    let schema_value: Value = serde_json::from_str(&schema)?;
+
+    // Create a validator for the schema
+    let validator = validator_for(&schema_value)?;
+
+    // Validate the dataset against the schema
+    let result = validator.iter_errors(&value);
+    let mut errors: Vec<ValidationError> = Vec::new();
+
+    for err in result {
+        errors.push(ValidationError::from(err));
+    }
+
+    Ok(errors)
+}
+
+/// Enum representing the different types of dataset inputs.
+pub enum DatasetInput {
+    Path(PathBuf),
+    Value(Value),
+    String(String),
+}
+
+impl From<PathBuf> for DatasetInput {
+    /// Converts a PathBuf into a DatasetInput.
+    fn from(path: PathBuf) -> Self {
+        DatasetInput::Path(path)
+    }
+}
+
+impl From<Value> for DatasetInput {
+    /// Converts a Value into a DatasetInput.
+    fn from(value: Value) -> Self {
+        DatasetInput::Value(value)
+    }
+}
+
+impl From<String> for DatasetInput {
+    /// Converts a String into a DatasetInput.
+    fn from(string: String) -> Self {
+        DatasetInput::String(string)
+    }
+}
+
+impl TryFrom<DatasetInput> for Value {
+    type Error = Box<dyn Error>;
+
+    fn try_from(input: DatasetInput) -> Result<Self, Self::Error> {
+        match input {
+            DatasetInput::Path(path) => {
+                // Logic to read from the path and convert to Value
+                let content = std::fs::read_to_string(path)?;
+                let value: Value = serde_json::from_str(&content)?;
+                Ok(value)
+            }
+            DatasetInput::Value(value) => Ok(value),
+            DatasetInput::String(string) => {
+                let value: Value = serde_json::from_str(&string)?;
+                Ok(value)
+            }
+        }
+    }
+}

src/lib.rs

@@ -41,6 +41,7 @@ pub mod json {
     mod datatype;
     pub mod export;
     pub mod schema;
+    pub mod validation;
 }
 
 pub(crate) mod markdown {

src/pipeline.rs

@@ -340,7 +340,7 @@ fn serialize_to_internal_schema(
 ) -> Result<(), Box<dyn Error>> {
     match merge_state {
         MergeState::Merge => {
-            let schema = model.sdrdm_schema();
+            let schema = model.internal_schema();
             save_to_file(out, &schema)?;
             print_render_msg(out, &Templates::Internal);
             Ok(())