mdmodels-core 0.1.7 → 0.2.0

package/README.md

@@ -1,13 +1,25 @@
-
 # MD-Models
 
-![Build Status](https://github.com/JR-1991/sdrdm.rs/actions/workflows/test.yml/badge.svg)
+![Crates.io Version](https://img.shields.io/crates/v/mdmodels) ![NPM Version](https://img.shields.io/npm/v/mdmodels-core)
+![PyPI - Version](https://img.shields.io/pypi/v/mdmodels-core)
+ ![Build Status](https://github.com/JR-1991/sdrdm.rs/actions/workflows/test.yml/badge.svg) 
 
-Welcome to Markdown Models (MD-Models), a powerful framework for research data management that prioritizes flexibility and efficiency.
+Welcome to Markdown Models (MD-Models), a powerful framework for research data management that prioritizes narrative and readability for data models.
 
 With an adaptable markdown-based schema language, MD-Models automatically generates schemas and programming language representations. This markdown schema forms the foundation for object-oriented models, enabling seamless cross-format compatibility and simplifying modifications to data structures.
 
-Check out the [documentation](https://fairchemistry.github.io/md-models/) for more information.
+## Core Philosophy
+
+The primary motivation behind MD-Models is to reduce cognitive overhead and maintenance burden by unifying documentation and structural definition into a single source of truth. Traditional approaches often require maintaining separate artifacts:
+
+1. Technical schemas (JSON Schema, XSD, ShEx, SHACL)
+2. Programming language implementations
+3. Documentation for domain experts
+4. API documentation
+
+This separation frequently leads to documentation drift and increases the cognitive load on both developers and domain experts.
+
+Check out the [documentation and graph editor](https://mdmodels.vercel.app/?about) for more information.
 
 ### Example
 
@@ -71,10 +83,42 @@ The following templates are available:
 - `python-dataclass`: Python dataclass implementation with JSON-LD support
 - `python-pydantic`: PyDantic implementation with JSON-LD support
 - `python-pydantic-xml`: PyDantic implementation with XML support
+- `typescript`: TypeScript interface definitions with JSON-LD support
+- `typescript-zod`: TypeScript Zod schema definitions
+- `rust`: Rust struct definitions with serde support
+- `golang`: Go struct definitions
+- `protobuf`: Protocol Buffer schema definition
+- `graphql`: GraphQL schema definition
 - `xml-schema`: XML schema definition
 - `json-schema`: JSON schema definition
+- `json-schema-all`: Multiple JSON schema definitions (one per object)
 - `shacl`: SHACL shapes definition
 - `shex`: ShEx shapes definition
+- `compact-markdown`: Compact markdown representation
+- `mkdocs`: MkDocs documentation format
+- `linkml`: LinkML schema definition
+
+## Installation options
+
+The main Rust crate is compiled to Python and WebAssembly, allowing the usage beyond the command line tool. These are the main packages:
+
+- **[Core Python Package](https://pypi.org/project/mdmodels-core/)**: Install via pip:
+  ```bash
+  # Mainly used to access the core functionality of the library
+  pip install mdmodels-core
+  ```
+
+- **[Python Package](https://github.com/FAIRChemistry/py-mdmodels/tree/master)**: Install via pip:
+  ```bash
+  # Provides in-memory data models, database support, LLM support, etc.
+  pip install mdmodels
+  ```
+
+- **[NPM Package](https://www.npmjs.com/package/mdmodels-core)**: Install via npm:
+  ```bash
+  # Mainly used to access the core functionality of the library
+  npm install mdmodels-core
+  ```
 
 ## Development
 

package/mdmodels-core.d.ts

@@ -9,11 +9,9 @@
  *
  * # Returns
  *
- * A `Result` which is:
- * - `Ok(JsValue)` if the parsing and serialization are successful.
- * - `Err(JsValue)` if there is an error during parsing or serialization.
+ * A `DataModel` or an error `JsError`.
  */
-export function parse_model(markdown_content: string): any;
+export function parse_model(markdown_content: string): DataModel;
 /**
  * Converts the given markdown content into a specified template format.
  *
@@ -46,7 +44,7 @@ export function convert_to(markdown_content: string, template: Templates): strin
  */
 export function json_schema(markdown_content: string, root: string | undefined, openai: boolean): string;
 /**
- * Validates the given markdown content and returns the validation result as a `JsValue`.
+ * Validates the given markdown content and returns the validation result as a `Validator`.
  *
  * # Arguments
  *
@@ -54,11 +52,9 @@ export function json_schema(markdown_content: string, root: string | undefined,
  *
  * # Returns
  *
- * A `Result` which is:
- * - `Ok(JsValue)` if the validation is successful.
- * - `Err(JsValue)` if there is an error during parsing or validation.
+ * Either an empty `Validator` or an error `Validator`.
  */
-export function validate(markdown_content: string): any;
+export function validate(markdown_content: string): Validator;
 /**
  * Enumeration of available templates.
  */
@@ -76,4 +72,225 @@ export enum Templates {
   MkDocs = 10,
   Internal = 11,
   Typescript = 12,
+  TypescriptZod = 13,
+  Rust = 14,
+  Protobuf = 15,
+  Graphql = 16,
+  Golang = 17,
+  Linkml = 18,
+}
+/**
+ * Validator for checking the integrity of a data model.
+ */
+export interface Validator {
+    is_valid: boolean;
+    errors: ValidationError[];
+}
+
+/**
+ * Enum representing the type of validation error.
+ */
+export type ErrorType = "NameError" | "TypeError" | "DuplicateError" | "GlobalError";
+
+/**
+ * Represents a validation error in the data model.
+ */
+export interface ValidationError {
+    message: string;
+    object: string | undefined;
+    attribute: string | undefined;
+    location: string;
+    error_type: ErrorType;
+    positions: Position[];
+}
+
+export interface PositionRange {
+    start: number;
+    end: number;
+}
+
+export interface Position {
+    line: number;
+    column: PositionRange;
+    offset: PositionRange;
+}
+
+/**
+ * Represents the front matter data of a markdown file.
+ */
+export interface FrontMatter {
+    /**
+     * A boolean field with a default value, renamed from `id-field`.
+     */
+    "id-field"?: boolean;
+    /**
+     * Optional hashmap of prefixes.
+     */
+    prefixes: Map<string, string> | undefined;
+    /**
+     * Optional namespace map.
+     */
+    nsmap: Map<string, string> | undefined;
+    /**
+     * A string field with a default value representing the repository URL.
+     */
+    repo?: string;
+    /**
+     * A string field with a default value representing the prefix.
+     */
+    prefix?: string;
+}
+
+export type DataType = { Boolean: boolean } | { Integer: number } | { Float: number } | { String: string };
+
+/**
+ * Represents an attribute with various properties and options.
+ */
+export interface Attribute {
+    /**
+     * The name of the attribute.
+     */
+    name: string;
+    /**
+     * Indicates if the attribute is an array.
+     */
+    multiple: boolean;
+    /**
+     * Is an identifier or not
+     */
+    is_id: boolean;
+    /**
+     * Data types associated with the attribute.
+     */
+    dtypes: string[];
+    /**
+     * Documentation string for the attribute.
+     */
+    docstring: string;
+    /**
+     * List of additional options for the attribute.
+     */
+    options: AttrOption[];
+    /**
+     * Term associated with the attribute, if any.
+     */
+    term: string | undefined;
+    /**
+     * Indicates if the attribute is required.
+     */
+    required: boolean;
+    /**
+     * Default value for the attribute.
+     */
+    default?: DataType;
+    /**
+     * XML type information for the attribute.
+     */
+    xml?: XMLType;
+    /**
+     * Is an enumeration or not
+     */
+    is_enum: boolean;
+    /**
+     * The line number of the attribute
+     */
+    position: Position | undefined;
 }
+
+export interface DataModel {
+    name?: string;
+    objects: Object[];
+    enums: Enumeration[];
+    config?: FrontMatter;
+}
+
+/**
+ * Represents an enumeration with a name and mappings.
+ */
+export interface Enumeration {
+    /**
+     * Name of the enumeration.
+     */
+    name: string;
+    /**
+     * Mappings associated with the enumeration.
+     */
+    mappings: Map<string, string>;
+    /**
+     * Documentation string for the enumeration.
+     */
+    docstring: string;
+    /**
+     * The line number of the enumeration
+     */
+    position: Position | undefined;
+}
+
+/**
+ * Represents an object with a name, attributes, docstring, and an optional term.
+ */
+export interface Object {
+    /**
+     * Name of the object.
+     */
+    name: string;
+    /**
+     * List of attributes associated with the object.
+     */
+    attributes: Attribute[];
+    /**
+     * Documentation string for the object.
+     */
+    docstring: string;
+    /**
+     * Optional term associated with the object.
+     */
+    term?: string;
+    /**
+     * Parent object of the object.
+     */
+    parent?: string;
+    /**
+     * The line number of the object
+     */
+    position?: Position;
+}
+
+/**
+ * Represents an XML type, either an attribute or an element.
+ */
+export type XMLType = { Attribute: { is_attr: boolean; name: string } } | { Element: { is_attr: boolean; name: string } };
+
+/**
+ * A raw key-value representation of an attribute option.
+ *
+ * This struct provides a simple string-based representation of options,
+ * which is useful for serialization/deserialization and when working
+ * with untyped data.
+ */
+export interface RawOption {
+    /**
+     * The key/name of the option
+     */
+    key: string;
+    /**
+     * The string value of the option
+     */
+    value: string;
+}
+
+/**
+ * Represents an option for an attribute in a data model.
+ *
+ * This enum provides a strongly-typed representation of various attribute options
+ * that can be used to configure and constrain attributes in a data model.
+ *
+ * The options are grouped into several categories:
+ * - JSON Schema validation options (e.g., minimum/maximum values, length constraints)
+ * - SQL database options (e.g., primary key)
+ * - LinkML specific options (e.g., readonly, recommended)
+ * - Custom options via the `Other` variant
+ *
+ */
+export type AttrOption = { Example: string } | { MinimumValue: number } | { MaximumValue: number } | { MinItems: number } | { MaxItems: number } | { MinLength: number } | { MaxLength: number } | { Pattern: string } | { Unique: boolean } | { MultipleOf: number } | { ExclusiveMinimum: number } | { ExclusiveMaximum: number } | { PrimaryKey: boolean } | { ReadOnly: boolean } | { Recommended: boolean } | { Other: { key: string; value: string } };
+

package/mdmodels-core_bg.js

@@ -105,11 +105,9 @@ function takeFromExternrefTable0(idx) {
  *
  * # Returns
  *
- * A `Result` which is:
- * - `Ok(JsValue)` if the parsing and serialization are successful.
- * - `Err(JsValue)` if there is an error during parsing or serialization.
+ * A `DataModel` or an error `JsError`.
  * @param {string} markdown_content
- * @returns {any}
+ * @returns {DataModel}
  */
 export function parse_model(markdown_content) {
     const ptr0 = passStringToWasm0(markdown_content, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
@@ -205,7 +203,7 @@ export function json_schema(markdown_content, root, openai) {
 }
 
 /**
- * Validates the given markdown content and returns the validation result as a `JsValue`.
+ * Validates the given markdown content and returns the validation result as a `Validator`.
  *
  * # Arguments
  *
@@ -213,25 +211,20 @@ export function json_schema(markdown_content, root, openai) {
  *
  * # Returns
  *
- * A `Result` which is:
- * - `Ok(JsValue)` if the validation is successful.
- * - `Err(JsValue)` if there is an error during parsing or validation.
+ * Either an empty `Validator` or an error `Validator`.
  * @param {string} markdown_content
- * @returns {any}
+ * @returns {Validator}
  */
 export function validate(markdown_content) {
     const ptr0 = passStringToWasm0(markdown_content, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
     const len0 = WASM_VECTOR_LEN;
     const ret = wasm.validate(ptr0, len0);
-    if (ret[2]) {
-        throw takeFromExternrefTable0(ret[1]);
-    }
-    return takeFromExternrefTable0(ret[0]);
+    return ret;
 }
 
 /**
  * Enumeration of available templates.
- * @enum {0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12}
+ * @enum {0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18}
  */
 export const Templates = Object.freeze({
     XmlSchema: 0, "0": "XmlSchema",
@@ -247,6 +240,12 @@ export const Templates = Object.freeze({
     MkDocs: 10, "10": "MkDocs",
     Internal: 11, "11": "Internal",
     Typescript: 12, "12": "Typescript",
+    TypescriptZod: 13, "13": "TypescriptZod",
+    Rust: 14, "14": "Rust",
+    Protobuf: 15, "15": "Protobuf",
+    Graphql: 16, "16": "Graphql",
+    Golang: 17, "17": "Golang",
+    Linkml: 18, "18": "Linkml",
 });
 
 export function __wbg_String_8f0eb39a4a4c2f66(arg0, arg1) {
@@ -257,10 +256,6 @@ export function __wbg_String_8f0eb39a4a4c2f66(arg0, arg1) {
     getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
 };
 
-export function __wbg_log_bdcc137b879aea04(arg0, arg1) {
-    console.log(getStringFromWasm0(arg0, arg1));
-};
-
 export function __wbg_new_254fa9eac11932ae() {
     const ret = new Array();
     return ret;
@@ -294,6 +289,11 @@ export function __wbindgen_bigint_from_i64(arg0) {
     return ret;
 };
 
+export function __wbindgen_bigint_from_u64(arg0) {
+    const ret = BigInt.asUintN(64, arg0);
+    return ret;
+};
+
 export function __wbindgen_error_new(arg0, arg1) {
     const ret = new Error(getStringFromWasm0(arg0, arg1));
     return ret;

package/package.json

@@ -5,7 +5,7 @@
     "Jan Range <jan.range@simtech.uni-stuttgart.de>"
   ],
   "description": "A tool to generate models, code and schemas from markdown files",
-  "version": "0.1.7",
+  "version": "0.2.0",
   "license": "MIT",
   "repository": {
     "type": "git",