test(loris): Update test to use real data

docs/user_guide/index.md

@@ -1,3 +1,10 @@
 # User Guide
 
 This section provides a detailed guide to using the `reproschema` command-line interface (CLI).
+
+It covers the following topics:
+- [Reproschema to REDCap](reproschema2redcap.md)
+- [REDCap to Reproschema](redcap2reproschema.md)
+- [LORIS to Reproschema](loris2reproschema.md)
+- [Output to REDCap](output2redcap.md)
+- [Reproschema to FHIR](reproschema2fhir.md)

docs/user_guide/loris2reproschema.md

@@ -0,0 +1,55 @@
+# LORIS to ReproSchema Conversion
+
+The `reproschema loris2reproschema` command converts a LORIS data dictionary in CSV format to the ReproSchema format.
+
+## Usage
+
+```bash
+reproschema loris2reproschema [OPTIONS] CSV_FILE CONFIG_FILE
+```
+
+### Arguments
+
+- `CSV_FILE`: Path to the LORIS data dictionary CSV file. (Required)
+- `CONFIG_FILE`: Path to the YAML configuration file. (Required)
+
+### Options
+
+- `--output-path PATH`: Path to the output directory. Defaults to the current directory.
+- `--encoding TEXT`: Encoding to use for reading the CSV file (e.g., `utf-8`, `latin-1`).
+- `--analyze`: Only analyze the CSV file structure and exit without conversion.
+- `--verbose`: Enable verbose logging.
+- `--help`: Show the help message and exit.
+
+## Configuration File
+
+The conversion process is controlled by a YAML configuration file. This file specifies how to map the columns in your LORIS CSV to ReproSchema fields, and provides metadata for the protocol.
+
+Here is an example of a configuration file:
+
+```yaml
+# Protocol information
+protocol_name: "HBCD_LORIS"
+protocol_display_name: "HEALthy Brain and Child Development Study"
+protocol_description: "Protocol for the HBCD study using LORIS data dictionary"
+loris_version: "1.0.0"
+
+# Column mappings from LORIS CSV to ReproSchema
+column_mappings:
+  activity_name: "full_instrument_name"
+  item_name: "name"
+  question: "question"
+  field_type: "field_type"
+  response_option_labels: "option_labels"
+  response_option_values: "option_values"
+```
+
+## Example
+
+To convert a LORIS CSV file named `HBCD_LORIS.csv` using a configuration file `hbcd-loris.yml`, you would run:
+
+```bash
+reproschema loris2reproschema HBCD_LORIS.csv hbcd-loris.yml --output-path my-protocol
+```
+
+This will create a new directory named `my-protocol/HBCD_LORIS` containing the ReproSchema representation of your protocol.

mkdocs.yml

@@ -7,6 +7,7 @@ nav:
     - CLI Usage: user_guide/cli_usage.md
     - Reproschema to REDCap: user_guide/reproschema2redcap.md
     - REDCap to Reproschema: user_guide/redcap2reproschema.md
+    - LORIS to Reproschema: user_guide/loris2reproschema.md
     - Output to REDCap: user_guide/output2redcap.md
     - Reproschema to FHIR: user_guide/reproschema2fhir.md
   - About: about.md

reproschema/cli.py

@@ -173,6 +173,50 @@ def redcap2reproschema(csv_path, yaml_path, output_path):
         raise click.ClickException(f"Error during conversion: {e}")
 
 
+@main.command()
+@click.argument("csv_file", type=click.Path(exists=True, dir_okay=False))
+@click.argument("config_file", type=click.Path(exists=True, dir_okay=False))
+@click.option(
+    "--output-path",
+    type=click.Path(dir_okay=True, writable=True, resolve_path=True),
+    default=".",
+    show_default=True,
+    help="Path to the output directory, defaults to the current directory.",
+)
+@click.option(
+    "--encoding",
+    help="Encoding to use for reading the CSV file (e.g., utf-8, latin-1).",
+)
+@click.option(
+    "--analyze",
+    is_flag=True,
+    help="Only analyze the CSV file structure and exit without conversion.",
+)
+@click.option(
+    "--verbose",
+    is_flag=True,
+    help="Enable verbose logging.",
+)
+def loris2reproschema(
+    csv_file, config_file, output_path, encoding, analyze, verbose
+):
+    """
+    Converts LORIS CSV files to Reproschema format.
+    """
+    from .loris2reproschema import loris2reproschema as loris2rs
+
+    try:
+        loris2rs(
+            csv_file, config_file, output_path, encoding, analyze, verbose
+        )
+        if not analyze:
+            click.echo(
+                "Converted LORIS data dictionary to Reproschema format."
+            )
+    except Exception as e:
+        raise click.ClickException(f"Error during conversion: {e}")
+
+
 @main.command()
 @click.argument("input_path", type=click.Path(exists=True, dir_okay=True))
 @click.argument("output_csv_path", type=click.Path(writable=True))

reproschema/example/loris/hbcd-loris.yml

@@ -0,0 +1,65 @@
+# HBCD LORIS Configuration
+
+# Protocol information
+protocol_name: "HBCD_LORIS"
+protocol_display_name: "HEALthy Brain and Child Development Study"
+protocol_description: "Protocol for the HBCD study using LORIS data dictionary"
+loris_version: "1.0.0"
+protocol_preamble: "This protocol contains the HBCD assessment instruments from the LORIS data dictionary"
+
+# Domain/instrument column settings
+domain_column: "full_instrument_name"
+fallback_domain_column: "domain"
+default_domain: "General"
+
+# Schema context URL (defaults to ReproSchema standard URL if not specified)
+schema_context_url: "https://raw.githubusercontent.com/ReproNim/reproschema/main/releases/1.0.0/reproschema"
+
+# Column mappings - customized based on HBCD LORIS CSV format
+column_mappings:
+  # Main identifiers and structure
+  activity_name: "full_instrument_name"    # Primary grouping field
+  item_name: "name"                        # Field identifier
+  question: "question"                     # Question text
+
+  # Input type and validation
+  field_type: "field_type"                 # Type of input (dropdown, text, etc.)
+  validation: "data_type"                  # Data type validation
+  required: "loris_required"               # If field is required
+
+  # Response options
+  response_option_labels: "option_labels"  # Labels for choices
+  response_option_values: "option_values"  # Values for choices
+
+  # Additional metadata
+  description: "description"               # Field description
+  min_value: "redcap_text_validation_min"  # Min value if applicable
+  max_value: "redcap_text_validation_max"  # Max value if applicable
+  visibility: "redcap_branching_logic"     # Conditional display logic
+  annotation: "redcap_field_annotation"    # Additional annotations
+  matrix_group: "redcap_matrix_group_name" # Matrix group name
+
+# Additional columns to include as notes in the schema
+additional_notes_fields:
+  - "source_field"
+  - "source_from"
+  - "source_respondent"
+  - "study"
+  - "data_type"
+  - "data_scope"
+  - "field_category"
+  - "field_class"
+  - "coding_format"
+  - "collection_platform"
+  - "collection_required"
+  - "description_status"
+
+# Field type overrides - map specific HBCD types to correct ReproSchema input types
+field_type_overrides:
+  "Dropdown": "select"
+  "Multi-select": "selectMultiple"
+  "Text": "text"
+  "Dropdown, Multi-select": "selectMultiple"
+
+# Enable verbose logging
+verbose: true