sof-mssql 1.0.0

package/LICENSE

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package/README.md

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+# SQL on FHIR views for Microsoft SQL Server
+
+A TypeScript library and CLI tool for loading FHIR into Microsoft SQL Server,
+and transpiling [SQL on FHIR](https://sql-on-fhir.org/) view definitions into
+T-SQL queries.
+
+## Features
+
+- **SQL on FHIR v2 compliance** - Implements
+  the [SQL on FHIR v2 specification](https://sql-on-fhir.org/ig/2.0.0/) for
+  transforming FHIR resources into tabular views
+- **FHIRPath support** - Full support for FHIRPath expressions in column
+  definitions and filters
+- **T-SQL optimisation** - Generates efficient T-SQL queries using `JSON_VALUE`,
+  `JSON_QUERY`, and `OPENJSON`
+- **forEach support** - Handles array flattening with `CROSS APPLY` for nested
+  FHIR resources
+- **Union support** - Supports `unionAll` for polymorphic fields
+- **Type casting** - Automatic SQL type inference and casting based on FHIR data
+  types
+- **WHERE clauses** - Supports view-level filtering with FHIRPath expressions
+- **Bulk NDJSON loader** - Built-in loader for importing FHIR resources from
+  NDJSON files
+
+## Quick start
+
+The easiest way to use sof-mssql is via `npx`:
+
+```bash
+# Load FHIR resources from NDJSON files
+npx sof-mssql load ./data --host localhost --user sa --password pass --database fhir
+
+# Transpile a ViewDefinition from stdin to stdout
+npx sof-mssql transpile <some.ViewDefinition.json >output.sql
+
+# Or use file arguments
+npx sof-mssql transpile --input some.ViewDefinition.json --output output.sql
+```
+
+## Installation
+
+For programmatic use, install via npm:
+
+```bash
+npm install sof-mssql
+```
+
+## CLI usage
+
+The CLI provides two main commands: `load` for bulk loading NDJSON files into
+SQL Server, and `transpile` for converting ViewDefinitions to T-SQL.
+
+### Loading NDJSON files
+
+Bulk load FHIR resources from NDJSON files into SQL Server:
+
+```bash
+# Load all NDJSON files from a directory
+npx sof-mssql load ./data \
+  --host localhost \
+  --user sa \
+  --password yourpassword \
+  --database fhir
+
+# Load with environment variables
+export MSSQL_HOST=localhost MSSQL_USER=sa MSSQL_PASSWORD=pass MSSQL_DATABASE=fhir
+npx sof-mssql load ./data
+
+# Load with custom table and batch settings
+npx sof-mssql load ./data \
+  --table-name my_resources \
+  --batch-size 5000 \
+  --parallel 2
+
+# Preview what would be loaded
+npx sof-mssql load ./data --dry-run
+```
+
+**File naming:** Files must follow the pattern `{ResourceType}.ndjson` (e.g.,
+`Patient.ndjson`, `Observation.ndjson`). The resource type is extracted from the
+filename and stored in the `resource_type` column.
+
+**Database options:**
+
+- `--host <host>` - Database server hostname
+- `--port <port>` - Database server port (default: 1433)
+- `--user <user>` - Database username
+- `--password <password>` - Database password
+- `--database <database>` - Database name
+- `--trust-server-certificate` - Trust server certificate
+
+**Loading options:**
+
+- `--table-name <name>` - Table name (default: `fhir_resources`)
+- `--schema-name <name>` - Schema name (default: `dbo`)
+- `--resource-type <type>` - Load only specific resource type
+- `--truncate` - Truncate table before loading
+- `--no-create-table` - Don't create table if it doesn't exist
+
+**Performance options:**
+
+- `--batch-size <size>` - Rows per batch (default: 1000)
+- `--parallel <count>` - Parallel file processing (default: 4, use 1-2 for best
+  reliability)
+
+**Output options:**
+
+- `--dry-run` - Preview without loading
+- `--verbose` - Show detailed progress
+- `--progress` - Show progress bar
+- `--quiet` - Minimal output
+- `--continue-on-error` - Continue if a file fails
+
+### Transpiling ViewDefinitions
+
+Convert SQL on FHIR ViewDefinitions to T-SQL:
+
+```bash
+# Read from stdin, write to stdout
+npx sof-mssql transpile <some.ViewDefinition.json
+
+# Read from file, write to stdout
+npx sof-mssql transpile --input some.ViewDefinition.json
+
+# Read from stdin, write to file
+npx sof-mssql transpile <some.ViewDefinition.json --output query.sql
+
+# Read from file, write to file
+npx sof-mssql transpile --input some.ViewDefinition.json --output query.sql
+
+# Fetch from remote server and transpile
+curl https://example.com/fhir/ViewDefinition/1 | npx sof-mssql transpile
+```
+
+**Options:**
+
+- `-i, --input <file>` - Input ViewDefinition JSON file (default: stdin)
+- `-o, --output <file>` - Output SQL file (default: stdout)
+
+**Global options:**
+
+- `-V, --version` - Output the version number
+- `-h, --help` - Display help information
+
+### Using transpiled SQL
+
+Once you've transpiled a ViewDefinition to T-SQL, you can use it to create
+database views or tables.
+
+#### Creating a view
+
+Views provide a virtual table based on the query, recomputed each time the view
+is queried:
+
+```bash
+# Transpile ViewDefinition to SQL file
+npx sof-mssql transpile --input patient_demographics.json --output patient_demographics.sql
+
+# Connect to SQL Server and create the view
+sqlcmd -S localhost -U sa -P yourpassword -d fhir -Q "
+CREATE VIEW [dbo].[patient_demographics] AS
+$(cat patient_demographics.sql)
+"
+```
+
+Or directly in SQL Server Management Studio:
+
+```sql
+CREATE VIEW [dbo].[patient_demographics] AS
+SELECT r.id AS [id],
+  JSON_VALUE(r.json, '$.name[0].family') AS [family_name],
+  CAST(JSON_VALUE(r.json, '$.birthDate') AS DATETIME2) AS [birth_date]
+FROM [dbo].[fhir_resources] AS [r]
+WHERE [r].[resource_type] = 'Patient'
+```
+
+#### Creating a materialised table
+
+For better query performance, you can materialise the view results into a
+physical table:
+
+```sql
+-- Create and populate the table in one statement
+SELECT *
+INTO [dbo].[patient_demographics]
+FROM (
+    SELECT
+    r.id AS [id], JSON_VALUE(r.json, '$.name[0].family') AS [family_name], CAST (JSON_VALUE(r.json, '$.birthDate') AS DATETIME2) AS [birth_date]
+    FROM [dbo].[fhir_resources] AS [r]
+    WHERE [r].[resource_type] = 'Patient'
+) AS view_results
+```
+
+To refresh a materialised table after data changes:
+
+```sql
+-- Truncate and reload
+TRUNCATE TABLE [dbo].[patient_demographics];
+
+INSERT INTO [dbo].[patient_demographics]
+SELECT r.id AS [id],
+  JSON_VALUE(r.json, '$.name[0].family') AS [family_name],
+  CAST(JSON_VALUE(r.json, '$.birthDate') AS DATETIME2) AS [birth_date]
+FROM [dbo].[fhir_resources] AS [r]
+WHERE [r].[resource_type] = 'Patient'
+```
+
+## Programmatic usage
+
+### Basic usage
+
+```javascript
+import {SqlOnFhir} from 'sof-mssql';
+
+// Create an instance with default configuration
+const sqlOnFhir = new SqlOnFhir();
+
+// Transpile a ViewDefinition to T-SQL
+const viewDefinition = {
+  resourceType: 'ViewDefinition',
+  resource: 'Patient',
+  name: 'patient_demographics',
+  select: [
+    {
+      column: [
+        {
+          name: 'id',
+          path: 'id',
+          type: 'id'
+        },
+        {
+          name: 'family_name',
+          path: 'name.family',
+          type: 'string'
+        },
+        {
+          name: 'birth_date',
+          path: 'birthDate',
+          type: 'date'
+        }
+      ]
+    }
+  ]
+};
+
+const result = sqlOnFhir.transpile(viewDefinition);
+
+console.log(result.sql);
+// Output:
+// SELECT
+//   r.id AS [id],
+//   JSON_VALUE(r.json, '$.name[0].family') AS [family_name],
+//   CAST(JSON_VALUE(r.json, '$.birthDate') AS DATETIME2) AS [birth_date]
+// FROM [dbo].[fhir_resources] AS [r]
+// WHERE [r].[resource_type] = 'Patient'
+
+// Access column metadata
+console.log(result.columns);
+// Output:
+// [
+//   { name: 'id', type: 'NVARCHAR(64)', nullable: true },
+//   { name: 'family_name', type: 'NVARCHAR(MAX)', nullable: true },
+//   { name: 'birth_date', type: 'DATETIME2', nullable: true }
+// ]
+```
+
+### Custom table configuration
+
+```javascript
+const sqlOnFhir = new SqlOnFhir({
+  tableName: 'my_fhir_data',
+  schemaName: 'clinical',
+  resourceIdColumn: 'resource_id',
+  resourceJsonColumn: 'resource_data'
+});
+```
+
+### Working with ViewDefinition strings
+
+```javascript
+import {SqlOnFhir} from 'sof-mssql';
+
+const sqlOnFhir = new SqlOnFhir();
+
+// From JSON string
+const viewDefJson = JSON.stringify(viewDefinition);
+const result = sqlOnFhir.transpile(viewDefJson);
+
+// From FHIR resource (with resourceType)
+const fhirResource = {
+  resourceType: 'ViewDefinition',
+  // ... rest of ViewDefinition
+};
+const result2 = sqlOnFhir.transpile(fhirResource);
+```
+
+## Database setup
+
+### Table structure
+
+sof-mssql expects FHIR resources to be stored in a table with the following
+structure:
+
+```sql
+CREATE TABLE [dbo].[fhir_resources] (
+    [id] INT IDENTITY (1, 1) NOT NULL PRIMARY KEY,
+    [resource_type] NVARCHAR (64) NOT NULL,
+    [json] NVARCHAR (MAX) NOT NULL
+);
+
+-- Create an index on resource_type for efficient filtering by resource type
+CREATE INDEX [IX_fhir_resources_resource_type]
+    ON [dbo].[fhir_resources] ([resource_type]);
+```
+
+The generated queries use:
+
+- `resource_type` column for filtering by FHIR resource type (indexed for
+  performance)
+- `json` column containing the complete FHIR resource as JSON
+- SQL Server's JSON functions (`JSON_VALUE`, `JSON_QUERY`, `OPENJSON`) for data
+  extraction
+
+**Performance recommendation:** The index on `resource_type` is strongly
+recommended as every ViewDefinition query filters by resource type. Without this
+index, queries will perform full table scans.
+
+### Loading data
+
+The easiest way to populate your database is using the built-in NDJSON loader (
+see [Loading NDJSON files](#loading-ndjson-files) above), which automatically
+creates the table with the correct structure. All FHIR resources are stored in a
+single table (default: `fhir_resources`), with the resource type extracted from
+the filename.
+
+## Contributing
+
+Contributions are welcome! Please read our [CONTRIBUTING](CONTRIBUTING.md)
+and [CODE_OF_CONDUCT](CODE_OF_CONDUCT.md) documents for guidelines on how to
+get involved.
+
+## License
+
+Copyright © 2025, Commonwealth Scientific and Industrial Research Organisation
+(CSIRO) ABN 41 687 119 230. Licensed under
+the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).

package/dist/cli.d.ts

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+#!/usr/bin/env node
+/**
+ * CLI for SQL on FHIR tooling.
+ * Supports transpiling ViewDefinitions and loading NDJSON data.
+ */
+export {};
+//# sourceMappingURL=cli.d.ts.map

package/dist/cli.d.ts.map

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+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAEA;;;GAGG"}

package/dist/cli.js

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+#!/usr/bin/env node
+"use strict";
+/**
+ * CLI for SQL on FHIR tooling.
+ * Supports transpiling ViewDefinitions and loading NDJSON data.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+const commander_1 = require("commander");
+const fs_1 = require("fs");
+const index_js_1 = require("./index.js");
+const load_js_1 = require("./load.js");
+/**
+ * Read input from stdin or file.
+ */
+async function readInput(inputFile) {
+    if (inputFile) {
+        return (0, fs_1.readFileSync)(inputFile, "utf-8");
+    }
+    // Read from stdin.
+    const chunks = [];
+    for await (const chunk of process.stdin) {
+        chunks.push(chunk);
+    }
+    return Buffer.concat(chunks).toString("utf-8");
+}
+/**
+ * Write output to stdout or file.
+ */
+function writeOutput(sql, outputFile) {
+    if (outputFile) {
+        (0, fs_1.writeFileSync)(outputFile, sql, "utf-8");
+    }
+    else {
+        process.stdout.write(sql);
+    }
+}
+/**
+ * Create the transpile command (default behaviour).
+ */
+function createTranspileCommand() {
+    const command = new commander_1.Command("transpile");
+    command
+        .description("Transpile SQL on FHIR ViewDefinitions to T-SQL queries")
+        .option("-i, --input <file>", "Input ViewDefinition JSON file (default: stdin)")
+        .option("-o, --output <file>", "Output SQL file (default: stdout)")
+        .action(async (options) => {
+        try {
+            // Read ViewDefinition from stdin or file.
+            const input = await readInput(options.input);
+            // Parse and validate JSON.
+            const viewDefinition = JSON.parse(input);
+            // Transpile to SQL.
+            const sqlOnFhir = new index_js_1.SqlOnFhir();
+            const result = sqlOnFhir.transpile(viewDefinition);
+            // Write SQL to stdout or file.
+            writeOutput(result.sql, options.output);
+        }
+        catch (err) {
+            console.error(`Error: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    return command;
+}
+/**
+ * Main CLI entry point.
+ */
+async function main() {
+    const program = new commander_1.Command();
+    program
+        .name("sof-mssql")
+        .description("SQL on FHIR tooling for MS SQL Server")
+        .version("1.0.0");
+    // Add subcommands.
+    program.addCommand(createTranspileCommand());
+    program.addCommand((0, load_js_1.createLoadCommand)());
+    // Parse arguments.
+    await program.parseAsync(process.argv);
+    // If no command specified, show help.
+    if (process.argv.length <= 2) {
+        program.help();
+    }
+}
+void main();
+//# sourceMappingURL=cli.js.map

package/dist/cli.js.map

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package/dist/fhirpath/transpiler.d.ts

@@ -0,0 +1,18 @@
+/**
+ * FHIRPath expression transpiler to T-SQL.
+ * Converts FHIRPath expressions to equivalent T-SQL expressions for MS SQL Server.
+ */
+import { TranspilerContext } from "./visitor";
+export { TranspilerContext } from "./visitor";
+export declare class Transpiler {
+    /**
+     * Transpile a FHIRPath expression to T-SQL.
+     */
+    static transpile(expression: string, context: TranspilerContext): string;
+    private static parseExpression;
+    /**
+     * Get the SQL data type for a FHIRPath expression result.
+     */
+    static inferSqlType(fhirType?: string): string;
+}
+//# sourceMappingURL=transpiler.d.ts.map

package/dist/fhirpath/transpiler.d.ts.map

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