diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 68b3ce1..a367c95 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,9 @@
# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
+
+# excluding fixes for csv data files
+exclude: ".*\\.csv$"
+
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
@@ -26,7 +30,7 @@ repos:
rev: v2.4.0
hooks:
- id: codespell
- args: [--toml, pyproject.toml, --skip="CHANGELOG.md"]
+ args: [--toml, pyproject.toml, "--skip=CHANGELOG.md"]
additional_dependencies: [tomli]
# Format TOML files
diff --git a/reproschema/convertutils.py b/reproschema/convertutils.py
new file mode 100644
index 0000000..e8c2965
--- /dev/null
+++ b/reproschema/convertutils.py
@@ -0,0 +1,245 @@
+import re
+from pathlib import Path
+from typing import Any, Dict, List
+
+import yaml
+from bs4 import BeautifulSoup
+
+from .context_url import CONTEXTFILE_URL
+from .jsonldutils import get_context_version
+from .models import Activity, Item, Protocol, write_obj_jsonld
+
+PROTOCOL_KEYS_REQUIRED = [
+ "protocol_name",
+ "protocol_display_name",
+ "redcap_version",
+]
+
+
+def read_check_yaml_config(yaml_path: str) -> Dict[str, Any]:
+ """Read and check the YAML configuration file."""
+ try:
+ with open(yaml_path, "r", encoding="utf-8") as f:
+ protocol = yaml.safe_load(f)
+ except yaml.YAMLError as e:
+ raise ValueError(f"Invalid YAML file: {str(e)}")
+ if set(PROTOCOL_KEYS_REQUIRED) - set(protocol.keys()):
+ raise ValueError(
+ f"Missing required keys in YAML file: {set(PROTOCOL_KEYS_REQUIRED) - set(protocol.keys())}"
+ )
+ return protocol
+
+
+def normalize_condition(condition_str, field_type=None):
+ """Normalize condition strings with specific handling for calc fields."""
+
+ # Handle boolean values
+ if isinstance(condition_str, bool):
+ return condition_str
+ if isinstance(condition_str, str):
+ if condition_str.lower() == "true":
+ return True
+ if condition_str.lower() == "false":
+ return False
+
+ # Convert to string if needed
+ if not isinstance(condition_str, str):
+ try:
+ condition_str = str(condition_str)
+ except:
+ raise ValueError("Condition must be a string or boolean")
+
+ # Clean HTML
+ condition_str = BeautifulSoup(condition_str, "html.parser").get_text()
+ condition_str = condition_str.strip()
+
+ if condition_str is None:
+ return None
+
+ # Common operator normalizations for all types
+ operator_replacements = [
+ (r"\s*\+\s*", " + "), # Normalize spacing around +
+ (r"\s*-\s*", " - "), # Normalize spacing around -
+ (r"\s*\*\s*", " * "), # Normalize spacing around *
+ (r"\s*\/\s*", " / "), # Normalize spacing around /
+ (r"\s*\(\s*", "("), # Remove spaces after opening parenthesis
+ (r"\s*\)\s*", ")"), # Remove spaces before closing parenthesis
+ (r"\s*,\s*", ","), # Normalize spaces around commas
+ (r"\s+", " "), # Normalize multiple spaces
+ ]
+
+ # Apply operator normalizations first
+ for pattern, repl in operator_replacements:
+ condition_str = re.sub(pattern, repl, condition_str)
+
+ # Then apply type-specific replacements
+ if field_type in ["sql", "calc"]:
+ # For calc fields, just remove brackets from field references
+ condition_str = re.sub(r"\[([^\]]+)\]", r"\1", condition_str)
+ else:
+ # For branching logic
+ replacements = [
+ (r"\(([0-9]*)\)", r"___\1"),
+ (r"([^>|<])=", r"\1=="),
+ (r"\[([^\]]*)\]", r"\1"), # Remove brackets and extra spaces
+ (r"\bor\b", "||"),
+ (r"\band\b", "&&"),
+ (r'"', "'"),
+ ]
+ for pattern, repl in replacements:
+ condition_str = re.sub(pattern, repl, condition_str)
+
+ result = condition_str.strip()
+ return result
+
+
+def parse_html(input_string, default_language="en"):
+ """
+ Parse HTML content and extract language-specific text.
+
+ Args:
+ input_string: The HTML string to parse
+ default_language: Default language code (default: "en")
+
+ Returns:
+ dict: Dictionary of language codes to text content, or None if invalid
+ """
+ try:
+ result = {}
+
+ # Handle non-string input
+ if not isinstance(input_string, str):
+ try:
+ input_string = str(input_string)
+ except:
+ return None
+
+ # Clean input string
+ input_string = input_string.strip()
+ if not input_string:
+ return None
+
+ # Parse HTML
+ soup = BeautifulSoup(input_string, "html.parser")
+
+ # Find elements with lang attribute
+ lang_elements = soup.find_all(True, {"lang": True})
+
+ if lang_elements:
+ # Process elements with language tags
+ for element in lang_elements:
+ lang = element.get("lang", default_language).lower()
+ text = element.get_text(strip=True)
+ if text:
+ result[lang] = text
+
+ # If no text was extracted but elements exist, try getting default text
+ if not result:
+ text = soup.get_text(strip=True)
+ if text:
+ result[default_language] = text
+ else:
+ # No language tags found, use default language
+ text = soup.get_text(strip=True)
+ if text:
+ result[default_language] = text
+
+ return result if result else None
+
+ except Exception as e:
+ print(f"Error parsing HTML: {str(e)}, trying plain text")
+ # Try to return plain text if HTML parsing fails
+ try:
+ if isinstance(input_string, str) and input_string.strip():
+ return {default_language: input_string.strip()}
+ except:
+ raise ValueError(f"Invalid input for HTML parsing: {input_string}")
+
+
+def create_activity_schema(
+ activity_name: str,
+ activity_data: Dict[str, Any],
+ output_path: Path,
+ redcap_version: str,
+ contextfile_url: str = CONTEXTFILE_URL,
+):
+ json_ld = {
+ "category": "reproschema:Activity",
+ "id": f"{activity_name}_schema",
+ "prefLabel": {"en": activity_name},
+ "schemaVersion": get_context_version(contextfile_url),
+ "version": redcap_version,
+ "ui": {
+ "order": activity_data[
+ "order"
+ ], # TODO spr czy to jest "clean order" i "clean bl list"?
+ "addProperties": activity_data["addProperties"],
+ "shuffle": False,
+ },
+ }
+
+ if activity_data["compute"]:
+ json_ld["compute"] = activity_data["compute"]
+ if activity_data.get("preamble"):
+ json_ld["preamble"] = activity_data["preamble"]
+ act = Activity(**json_ld)
+ path = output_path / "activities" / activity_name
+ path.mkdir(parents=True, exist_ok=True)
+ write_obj_jsonld(
+ act,
+ path / f"{activity_name}_schema",
+ contextfile_url=contextfile_url,
+ )
+
+ items_path = path / "items"
+ items_path.mkdir(parents=True, exist_ok=True)
+
+ for item in activity_data["items"]:
+ item_path = items_path / item["id"]
+ item_path.parent.mkdir(parents=True, exist_ok=True)
+ write_obj_jsonld(
+ Item(**item), item_path, contextfile_url=CONTEXTFILE_URL
+ )
+ print(f"{activity_name} Instrument schema created")
+
+
+def create_protocol_schema(
+ protocol_data: Dict[str, Any],
+ activities: List[str],
+ output_path: Path,
+ contextfile_url: str = CONTEXTFILE_URL,
+):
+ protocol_name = protocol_data["protocol_name"].strip().replace(" ", "_")
+ protocol_schema = {
+ "category": "reproschema:Protocol",
+ "id": f"{protocol_name}_schema",
+ "prefLabel": {"en": protocol_data["protocol_display_name"]},
+ "description": {"en": protocol_data.get("protocol_description", "")},
+ "schemaVersion": get_context_version(contextfile_url),
+ "version": protocol_data["redcap_version"],
+ "ui": {
+ "addProperties": [
+ {
+ "isAbout": f"../activities/{activity}/{activity}_schema",
+ "variableName": f"{activity}_schema",
+ "prefLabel": {"en": activity.replace("_", " ").title()},
+ "isVis": True,
+ }
+ for activity in activities
+ ],
+ "order": [
+ f"../activities/{activity}/{activity}_schema"
+ for activity in activities
+ ],
+ "shuffle": False,
+ },
+ }
+
+ protocol_dir = output_path / protocol_name
+ protocol_dir.mkdir(parents=True, exist_ok=True)
+ write_obj_jsonld(
+ Protocol(**protocol_schema),
+ protocol_dir / f"{protocol_name}_schema",
+ contextfile_url=contextfile_url,
+ )
+ print(f"Protocol schema created in {protocol_dir}")
diff --git a/reproschema/redcap2reproschema.py b/reproschema/redcap2reproschema.py
index 8043a25..c6f0b20 100644
--- a/reproschema/redcap2reproschema.py
+++ b/reproschema/redcap2reproschema.py
@@ -1,937 +1,500 @@
-import os
import re
from pathlib import Path
+from typing import Any, Dict
-import numpy as np
import pandas as pd
-import yaml
-from bs4 import BeautifulSoup
from .context_url import CONTEXTFILE_URL
-from .jsonldutils import get_context_version
-from .models import Activity, Item, Protocol, write_obj_jsonld
-
-# All the mapping used in the code
-SCHEMA_MAP = {
- "Variable / Field Name": "@id", # column A
- # "Item Display Name": "prefLabel", # there is no column for this
- "Field Note": "description",
- # TODO: often "Field Annotation" has "@HIDDEN" and other markers
- # TODO: not sure if this can be every treated as description
- # "Field Annotation": "isVis", # column R
- "Section Header": "preamble", # column C (need double-check)
- "Field Label": "question", # column E
- "Field Type": "inputType", # column D
- "Allow": "allow", # TODO: I don't see this column in the examples
- "Required Field?": "valueRequired", # column M
- "Text Validation Min": "minValue", # column I
- "Text Validation Max": "maxValue", # column J
- "Choices, Calculations, OR Slider Labels": "choices", # column F
- "Branching Logic (Show field only if...)": "visibility", # column L
- "Custom Alignment": "customAlignment", # column N
- # "Identifier?": "identifiable", # column K # todo: should we remove the identifiers completely?
- "responseType": "@type", # not sre what to do with it
-}
-
-INPUT_TYPE_MAP = {
- "calc": "number",
- "sql": "number",
- "yesno": "radio",
- "radio": "radio",
- "checkbox": "radio",
- "descriptive": "static",
- "dropdown": "select",
- "text": "text",
- "notes": "text",
- "file": "documentUpload",
- "slider": "slider",
-}
-
-# Map certain field types directly to xsd types
-VALUE_TYPE_MAP = {
- "text": "xsd:string",
- "date_": "xsd:date",
- "date_mdy": "xsd:date", # ?? new one TODO: not sure what to do with it, it's not xsd:date
- "datetime_seconds_mdy": "xsd:date", # ?? new one TODO: not sure what to do with it, it's not xsd:date
- "date_ymd": "xsd:date", # new one
- "date_dmy": "xsd:date",
- "datetime_": "xsd:dateTime",
- "datetime_ymd": "xsd:dateTime",
- "time_": "xsd:time",
- "email": "xsd:string",
- "phone": "xsd:string",
- "number": "xsd:decimal", # new one (TODO: could be integer, but have no idea of knowing)
- "float": "xsd:decimal", # new one
- "integer": "xsd:integer", # new one
- "signature": "xsd: string", # ?? new one
- "zipcode": "xsd: string", # new one
- "autocomplete": "xsd: string", # ?? new one
-}
-
-# TODO: removing for now, since it's not used
-# TODO: inputType is treated separately,
-# TODO: I don't see allow and shuffle in the redcap csv
-# TODO: I don't know what to do with customAlignment
-# UI_LIST = ["shuffle", "allow", "customAlignment"]
-COMPUTE_LIST = ["calc", "sql"] # field types that should be used as compute
-# TODO: minValue and max Value can be smteims str, ignored for now
-RESPONSE_COND = ["minValue", "maxValue"]
-ADDITIONAL_NOTES_LIST = ["Field Note", "Question Number (surveys only)"]
-
-
-def clean_dict_nans(obj):
- """Remove NaN values from a dictionary."""
- if not isinstance(obj, dict):
- return obj
- return {k: v for k, v in obj.items() if pd.notna(v)}
-
-
-# TODO: normalized condition should depend on the field type, e.g., for SQL
-def normalize_condition(condition_str, field_type=None):
- """Normalize condition strings with specific handling for calc fields."""
- if condition_str is None or pd.isna(condition_str):
- return None
-
- # Handle boolean values
- if isinstance(condition_str, bool):
- return condition_str
- if isinstance(condition_str, str):
- if condition_str.lower() == "true":
- return True
- if condition_str.lower() == "false":
- return False
-
- # Convert to string if needed
- if not isinstance(condition_str, str):
- try:
- condition_str = str(condition_str)
- except:
- return None
-
- try:
-
- # Clean HTML
- condition_str = BeautifulSoup(condition_str, "html.parser").get_text()
- condition_str = condition_str.strip()
-
- if not condition_str:
- return None
-
- # Common operator normalizations for all types
- operator_replacements = [
- (r"\s*\+\s*", " + "), # Normalize spacing around +
- (r"\s*-\s*", " - "), # Normalize spacing around -
- (r"\s*\*\s*", " * "), # Normalize spacing around *
- (r"\s*\/\s*", " / "), # Normalize spacing around /
- (r"\s*\(\s*", "("), # Remove spaces after opening parenthesis
- (r"\s*\)\s*", ")"), # Remove spaces before closing parenthesis
- (r"\s*,\s*", ","), # Normalize spaces around commas
- (r"\s+", " "), # Normalize multiple spaces
- ]
-
- # Apply operator normalizations first
- for pattern, repl in operator_replacements:
- condition_str = re.sub(pattern, repl, condition_str)
-
- # Then apply type-specific replacements
- if field_type in ["sql", "calc"]:
- # For calc fields, just remove brackets from field references
- condition_str = re.sub(r"\[([^\]]+)\]", r"\1", condition_str)
- else:
- # For branching logic
- replacements = [
- (r"\(([0-9]*)\)", r"___\1"),
- (r"([^>|<])=", r"\1=="),
- (r"\[([^\]]*)\]", r"\1"), # Remove brackets and extra spaces
- (r"\bor\b", "||"),
- (r"\band\b", "&&"),
- (r'"', "'"),
- ]
- for pattern, repl in replacements:
- condition_str = re.sub(pattern, repl, condition_str)
-
- result = condition_str.strip()
- return result
-
- except Exception as e:
- print(f"Error normalizing condition: {str(e)}")
- return None
-
-
-def process_field_properties(data):
+from .convertutils import (
+ create_activity_schema,
+ create_protocol_schema,
+ normalize_condition,
+ parse_html,
+ read_check_yaml_config,
+)
+from .redcap_mappings import (
+ ADDITIONAL_NOTES_LIST,
+ COMPUTE_LIST,
+ INPUT_TYPE_MAP,
+ REDCAP_COLUMN_MAP,
+ REDCAP_COLUMN_REQUIRED,
+ RESPONSE_COND,
+ get_value_type,
+)
+
+
+def process_input_value_types(input_type_rc, value_type_rc) -> (str, str):
"""
- Process field properties from REDCap data dictionary to create a property object.
-
- This function extracts and processes field properties from a REDCap data dictionary row,
- handling variable names, visibility conditions, field annotations, required fields,
- and matrix group information.
+ Process input type and value type to determine the final input type and value type,
+ that can be used by ReproSchema.
Args:
- data (dict): A dictionary containing field data from the REDCap data dictionary.
- Expected keys include:
- - "Variable / Field Name": The field's variable name
- - "Branching Logic (Show field only if...)": Conditional display logic
- - "Field Annotation": Special field annotations (e.g., @READONLY, @HIDDEN)
- - "Required Field?": Whether the field is required
- - "Matrix Group Name": Matrix group identifier
- - "Matrix Ranking?": Matrix ranking information
-
- Returns:
- dict: A property object containing processed field information with the following structure:
- {
- "variableName": str, # The field's variable name
- "isAbout": str, # Reference to the item (e.g., "items/variable_name")
- "isVis": str/bool, # Visibility condition or False if hidden
- "valueRequired": bool, # Optional, present if field is required
- "matrixGroupName": str,# Optional, present if field is part of a matrix
- "matrixRanking": bool # Optional, present if matrix has ranking
- }
-
- Examples:
- >>> data = {
- ... "Variable / Field Name": "age",
- ... "Required Field?": "y",
- ... "Branching Logic (Show field only if...)": "[gender] = '1'"
- ... }
- >>> process_field_properties(data)
- {'variableName': 'age', 'isAbout': 'items/age', 'valueRequired': True, 'isVis': "gender == '1'"}
- """
- if not isinstance(data, dict):
- return {"variableName": "unknown", "isAbout": "items/unknown"}
-
- var_name = str(data.get("Variable / Field Name", "unknown")).strip()
- prop_obj = {"variableName": var_name, "isAbout": f"items/{var_name}"}
-
- # Handle required field consistently
- if data.get("Required Field?", "").strip().lower() == "y":
- prop_obj["valueRequired"] = True
-
- # Set isVis only when needed
- condition = data.get("Branching Logic (Show field only if...)")
- if pd.notna(condition):
- normalized = normalize_condition(condition)
- if normalized:
- prop_obj["isVis"] = normalized
-
- # Handle field annotations that affect visibility
- annotation = data.get("Field Annotation", "").strip().upper()
- if annotation:
- if (
- "@HIDDEN" in annotation
- or "@READONLY" in annotation
- or "@CALCTEXT" in annotation
- ):
- prop_obj["isVis"] = False
-
- field_type = data.get("Field Type", "").strip().lower()
- if field_type in ["calc", "sql"]:
- prop_obj["isVis"] = False
-
- matrix_group = data.get("Matrix Group Name")
- if pd.notna(matrix_group):
- prop_obj["matrixGroupName"] = str(matrix_group).strip()
- if pd.notna(data.get("Matrix Ranking?")):
- prop_obj["matrixRanking"] = data["Matrix Ranking?"]
-
- return prop_obj
-
-
-def parse_field_type_and_value(field):
- """
- Parse field type and determine appropriate value type.
-
- Args:
- field: Dictionary containing field information
+ input_type_rc (str): Input type from redcap form
+ value_type_rc (str): Value type from redcap form
Returns:
tuple: (input_type, value_type)
+ input_type (str): Final input type for ReproSchema
+ value_type (str): Final value type for ReproSchema
"""
- try:
- # Get and validate field type
- field_type = field.get("Field Type", "")
- if pd.isna(field_type):
- field_type = ""
- field_type = str(field_type).strip().lower()
-
- # Validate field type
- if field_type and field_type not in INPUT_TYPE_MAP:
- raise ValueError(
- f"Field type '{field_type}' is not currently supported, "
- f"supported types are: {', '.join(INPUT_TYPE_MAP.keys())}"
- )
-
- input_type = INPUT_TYPE_MAP.get(field_type, "text")
- value_type = "xsd:string" # Default value type
-
- # Get validation type
- validation_type = field.get(
- "Text Validation Type OR Show Slider Number"
+ # If input type in redcap is set but not recognized, raise an error
+ if input_type_rc not in INPUT_TYPE_MAP:
+ raise ValueError(
+ f"Input type '{input_type_rc}' from redcap is not currently supported, "
+ f"supported types are: {', '.join(INPUT_TYPE_MAP.keys())}"
)
- if pd.notna(validation_type):
- validation_type = str(validation_type).strip().lower()
-
- if validation_type:
- if validation_type not in VALUE_TYPE_MAP:
- raise ValueError(
- f"Validation type '{validation_type}' is not supported, "
- f"supported types are: {', '.join(VALUE_TYPE_MAP.keys())}"
- )
-
- value_type = VALUE_TYPE_MAP[validation_type]
-
- # Adjust input type based on validation
- if validation_type == "integer" and field_type == "text":
- input_type = "number"
- elif (
- validation_type in ["float", "number"]
- and field_type == "text"
- ):
- input_type = "float"
- elif validation_type == "email" and field_type == "text":
- input_type = "email"
- elif validation_type == "signature" and field_type == "text":
- input_type = "sign"
- elif value_type == "xsd:date" and field_type == "text":
- input_type = "date"
-
- elif field_type == "yesno":
- value_type = "xsd:boolean"
- elif field_type in COMPUTE_LIST:
- value_type = "xsd:integer"
-
- # Handle radio/select fields with choices
- if input_type in ["radio", "select", "slider"]:
- choices = field.get("Choices, Calculations, OR Slider Labels")
- if pd.notna(choices):
- _, value_types = process_choices(
- choices, field.get("Variable / Field Name", "unknown")
- )
- if value_types:
- value_type = value_types[
- 0
- ] # Use first value type if multiple exist
-
- return input_type, value_type
-
- except Exception as e:
- print(f"Error parsing field type: {str(e)}")
- return "text", "xsd:string" # Return defaults on error
-
-
-def process_choices(choices_str, field_name):
+ elif input_type_rc:
+ input_type = INPUT_TYPE_MAP.get(input_type_rc)
+
+ if value_type_rc:
+ # Get value type using the new function
+ value_type = get_value_type(value_type_rc)
+
+ # Adjust input type based on validation
+ if value_type == "xsd:date" and input_type_rc == "text":
+ input_type = "date"
+ elif value_type_rc == "integer" and input_type_rc == "text":
+ input_type = "number"
+ elif value_type_rc in ["float", "number"] and input_type_rc == "text":
+ input_type = "float"
+ elif value_type_rc == "email" and input_type_rc == "text":
+ input_type = "email"
+ elif value_type_rc == "signature" and input_type_rc == "text":
+ input_type = "sign"
+
+ elif input_type_rc == "yesno":
+ value_type = "xsd:boolean"
+ elif input_type_rc == "truefalse":
+ value_type = "xsd:boolean"
+ elif input_type_rc in COMPUTE_LIST:
+ value_type = "xsd:integer"
+ else: # if no validation type is set, default to string
+ value_type = "xsd:string"
+
+ return input_type, value_type
+
+
+def process_response_options(row, input_type_rc, value_type) -> Dict[str, Any]:
"""
- Process REDCap choice options into structured format.
+ Process response options from the row and return a dictionary of response options
Args:
- choices_str: String containing choice options
- field_name: Field name for error reporting
-
+ row (dict): Dictionary containing all fields from the redcap csv row
+ input_type_rc (str): Input type from redcap form
+ value_type (str): ReproSchema value type
Returns:
- tuple: (choices list, value types list) or (None, None) if invalid
+ dict: Response options
"""
- try:
- if pd.isna(choices_str) or not isinstance(choices_str, str):
- return None, None
+ input_type = INPUT_TYPE_MAP[input_type_rc]
+ # Default response options
+ response_options = {"valueType": [value_type]}
- choices_str = choices_str.strip()
- if not choices_str:
- return None, None
-
- choices = []
- choices_value_type = set()
-
- # Split choices by pipe
- choice_items = [c.strip() for c in choices_str.split("|") if c.strip()]
-
- if len(choice_items) < 1:
- print(f"Warning: No valid choices found in {field_name}")
- return None, None
+ # Handle specific input_type_rc that modify other properties (not only inputType and valueType)
+ if input_type_rc == "yesno":
+ response_options["choices"] = [
+ {"name": {"en": "Yes"}, "value": 1},
+ {"name": {"en": "No"}, "value": 0},
+ ]
+ elif input_type_rc == "truefalse":
+ response_options["choices"] = [
+ {"name": {"en": "True"}, "value": 1},
+ {"name": {"en": "False"}, "value": 0},
+ ]
+ elif input_type_rc == "checkbox":
+ response_options["multipleChoice"] = True
- for choice in choice_items:
- # Split on first comma only
- parts = choice.split(",", 1)
- if len(parts) < 2:
- print(
- f"Warning: Invalid choice format '{choice}' in {field_name}"
+ if row.get("choices") and input_type:
+ if input_type in ["radio", "select", "slider", "text"]:
+ choices, choices_val_type_l = process_choices(
+ row.get("choices"), item_name=row["item_name"]
+ )
+ if choices:
+ response_options.update(
+ {
+ "choices": choices,
+ "valueType": choices_val_type_l,
+ }
)
- continue
-
- value_part = parts[0].strip()
- label_part = parts[1].strip()
-
- if not label_part:
- print(
- f"Warning: Empty label in choice '{choice}' in {field_name}"
+ if input_type == "slider":
+ response_options.update(
+ {
+ "minValue": 0,
+ "maxValue": 100,
+ }
)
- continue
+ elif input_type_rc in COMPUTE_LIST:
+ pass # taken care below, it's not really choices
+ else:
+ print(
+ f"Warning/Error: Unexpected input type for choices in {row['item_name']}: input type {input_type} "
+ f"(original in redcap: {input_type_rc}), values: {row.get('choices')}"
+ )
+ # raise ValueError(
+ # f"Unexpected input type '{input_type}' (original in redcap: {input_type_rc}) "
+ # f"for item with choices in {item['item_name']}"
+ # )
- # Determine value type and convert value
+ for key in RESPONSE_COND:
+ if row.get(key) is not None and str(row.get(key)).strip():
try:
- # First try integer conversion
- if value_part == "0":
- value = 0
- value_type = "xsd:integer"
- elif value_part.isdigit() and value_part[0] == "0":
- value = value_part
- value_type = "xsd:string"
+ if value_type == "xsd:integer":
+ parsed_value = int(row[key])
+ elif value_type == "xsd:decimal":
+ parsed_value = float(row[key])
else:
- try:
- value = int(value_part)
- value_type = "xsd:integer"
- except ValueError:
- try:
- value = float(value_part)
- value_type = "xsd:decimal"
- except ValueError:
- value = value_part
- value_type = "xsd:string"
-
- choices_value_type.add(value_type)
-
- # Create choice object
- parsed_label = parse_html(label_part)
- choice_obj = {
- "name": (
- parsed_label if parsed_label else {"en": label_part}
- ),
- "value": value,
- }
- choices.append(choice_obj)
-
- except (ValueError, TypeError) as e:
+ print(
+ f"Warning: {key} is not supported for value types other than integer or decimal, value type provided is {value_type}"
+ )
+ continue
+ response_options[key] = parsed_value
+ except ValueError:
print(
- f"Warning: Error processing choice '{choice}' in {field_name}: {str(e)}"
+ f"Warning/Error: Value {row[key]} is not a valid {value_type}"
)
continue
+ return response_options
- if not choices:
- return None, None
- return choices, list(choices_value_type)
+def process_choices(choices_str, item_name):
+ if len(choices_str.split("|")) < 2:
+ print(
+ f"WARNING: {item_name}: I found only one option for choice: {choices_str}"
+ )
- except Exception as e:
- print(f"Error processing choices for {field_name}: {str(e)}")
- return None, None
+ choices = []
+ choices_value_type = set()
+ # Split choices by pipe
+ choice_items = [c.strip() for c in choices_str.split("|") if c.strip()]
-def parse_html(input_string, default_language="en"):
- """
- Parse HTML content and extract language-specific text.
+ if len(choice_items) < 1:
+ print(f"Warning: No valid choices found in {item_name}")
+ return None, None
- Args:
- input_string: The HTML string to parse
- default_language: Default language code (default: "en")
+ for choice in choice_items:
+ # Split on first comma only
+ parts = choice.split(",", 1)
+ if len(parts) < 2:
+ print(f"Warning: Invalid choice format '{choice}' in {item_name}")
+ parts = parts * 2 # assuming the same value as label
- Returns:
- dict: Dictionary of language codes to text content, or None if invalid
- """
- try:
- if pd.isna(input_string):
- return None
+ value_part = parts[0].strip()
+ label_part = parts[1].strip()
- result = {}
+ if not label_part:
+ print(f"Warning: Empty label in choice '{choice}' in {item_name}")
+ continue
- # Handle non-string input
- if not isinstance(input_string, str):
+ # Determine value type and convert value
+ if value_part == "0":
+ value = 0
+ value_type = "xsd:integer"
+ elif (
+ value_part.isdigit() and value_part[0] == "0"
+ ): # and not choices_value_type.union({"xsd:decimal", "xsd:integer"}):
+ value = value_part
+ value_type = "xsd:string"
+ else:
try:
- input_string = str(input_string)
- except:
- return None
-
- # Clean input string
- input_string = input_string.strip()
- if not input_string:
- return None
-
- # Parse HTML
- soup = BeautifulSoup(input_string, "html.parser")
-
- # Find elements with lang attribute
- lang_elements = soup.find_all(True, {"lang": True})
+ value = int(value_part)
+ value_type = "xsd:integer"
+ except ValueError:
+ try:
+ value = float(value_part)
+ value_type = "xsd:decimal"
+ except ValueError:
+ value = value_part
+ value_type = "xsd:string"
+ choices_value_type.add(value_type)
- if lang_elements:
- # Process elements with language tags
- for element in lang_elements:
- lang = element.get("lang", default_language).lower()
- text = element.get_text(strip=False)
- if text:
- result[lang] = text
+ # Create choice object
+ choice_obj = {
+ "name": parse_html(label_part) or {"en": label_part},
+ "value": value,
+ }
+ choices.append(choice_obj)
+ # sorting to make sure the order is consistent
+ choices_value_type = list(choices_value_type)
+ choices_value_type.sort()
+ return (choices, choices_value_type) if choices else (None, None)
- # If no text was extracted but elements exist, try getting default text
- if not result:
- text = soup.get_text(strip=False)
- if text:
- result[default_language] = text
- else:
- # No language tags found, use default language
- text = soup.get_text(strip=False)
- if text:
- result[default_language] = text
- return result if result else None
+def process_preamble(
+ row, prior_preamble_info, input_type_rc
+) -> (str, Dict[str, str]):
+ """
+ Function to get preamble information from the row and preamble from the previous row.
+ The preamble will be propagated it if necessary.
+ Args:
+ row: Dictionary containing all fields from the redcap csv row
+ prior_preamble_info: Dictionary containing preamble information from the previous row
+ input_type_rc: Original input type from redcap form
- except Exception as e:
- print(f"Error parsing HTML: {str(e)}")
- # Try to return plain text if HTML parsing fails
- try:
- if isinstance(input_string, str) and input_string.strip():
- return {default_language: input_string.strip()}
- except:
- pass
- return None
+ Returns:
+ tuple: (item_preamble, preamble_info_propagate)
+ item_preamble: Preamble text for the current item
+ preamble_info_propagate: Dictionary containing preamble information to propagate to the next item
+ """
+ preamble, preamble_gr, preamble_ind = None, None, None
+ # checking if preamble is set in the current row
+ if row.get("preamble") and str(row.get("preamble")).strip():
+ preamble = parse_html(row["preamble"])
+ # setting the preamble index to 0 for new preamble
+ preamble_ind = 0
+ # checking if a group is set in the current row
+ if row.get("matrixGroup") and str(row.get("matrixGroup")).strip():
+ preamble_gr = str(row.get("matrixGroup")).strip()
+ # if group is not set, and the item is a descriptive type, I use preamble only for this row, will not be propagated
+ elif input_type_rc == "descriptive":
+ preamble_ind = None
+ # if there is no preamble in the current row, check if there is a preamble from the previous row to propagate
+ elif prior_preamble_info and prior_preamble_info.get("preamble"):
+ preamble_previous, preamble_gr_previous, preamble_ind_previous = [
+ prior_preamble_info[key] for key in ["preamble", "group", "index"]
+ ]
+ # if there is no group set in the previous row, propagate the preamble
+ if preamble_gr_previous is None:
+ preamble = preamble_previous
+ # sometimes the group is set in the row after the preamble, so check again for the group
+ if preamble_ind_previous == 0:
+ if (
+ row.get("matrixGroup")
+ and str(row.get("matrixGroup")).strip()
+ ):
+ preamble_gr = str(row.get("matrixGroup")).strip()
+ preamble_ind = preamble_ind_previous + 1
+ # if the preamble from the previous row is set to the specific group, the current row should be in the same group
+ elif (
+ row.get("matrixGroup")
+ and str(row.get("matrixGroup")).strip() == preamble_gr_previous
+ ):
+ preamble = preamble_previous
+ preamble_gr = preamble_gr_previous
+ preamble_ind = preamble_ind_previous + 1
+
+ # setting the preamble used for the specific row/item
+ if preamble:
+ item_preamble = preamble
+ else:
+ item_preamble = None
+
+ # setting preamble information to propagate to the next item
+ if preamble and preamble_ind is not None:
+ preamble_info_propagate = {
+ "preamble": preamble,
+ "group": preamble_gr,
+ "index": preamble_ind,
+ }
+ else:
+ preamble_info_propagate = None
+ return item_preamble, preamble_info_propagate
def process_row(
- abs_folder_path,
- schema_context_url,
- form_name,
- field,
- add_preamble=True,
-):
- """Process a row of the REDCap data and generate the jsonld file for the item."""
- item_id = field.get(
- "Variable / Field Name", ""
- ) # item_id should always be the Variable name in redcap
- rowData = {
+ row: Dict[str, Any], prior_preamble_info=None
+) -> (Dict[str, Any], Dict[str, str], Dict[str, Any], Dict[str, Any]):
+ """
+ Process a single row of the CSV and return structured data for an item,
+ preamble information that can be propagated to the next item.
+ It also collects information needed for activity schema.
+ Args:
+ row: Dictionary containing all fields from the redcap csv row
+ prior_preamble_info: Dictionary containing preamble information from the previous row
+
+ Returns:
+ tuple: (item_data, preamble_info_propagate, compute, addProperties)
+ item_data: Dictionary containing structured data for the item
+ preamble_info_propagate: Dictionary containing preamble information to propagate to the next item
+ compute: Dictionary containing compute information for the activity schema
+ addProperties: Dictionary containing additional properties for the activity schema
+ """
+ # processing input type and value type that will be used by reproschema, and original one from redcap
+ input_type_rc = str(row.get("inputType", "")).strip().lower()
+ value_type_rc = str(row.get("validation", "")).strip().lower()
+ if not input_type_rc:
+ input_type_rc = "text"
+
+ input_type, value_type = process_input_value_types(
+ input_type_rc, value_type_rc
+ )
+ item_data = {
"category": "reproschema:Item",
- "id": item_id,
- "prefLabel": {"en": item_id}, # there is no prefLabel in REDCap
- # "description": {"en": f"{item_id} of {form_name}"},
+ "id": row["item_name"],
+ "prefLabel": {"en": row["item_name"]},
+ "question": parse_html(row["question"]),
+ "ui": {"inputType": input_type},
}
- field_type = field.get("Field Type")
- if pd.isna(field_type):
- field_type = ""
- input_type, value_type = parse_field_type_and_value(field)
-
- # Initialize ui object with common properties
- ui_obj = {"inputType": input_type}
+ item_data["responseOptions"] = process_response_options(
+ row, input_type_rc, value_type
+ )
- # Handle readonly status first - this affects UI behavior
- annotation = field.get("Field Annotation")
- if annotation is not None and not pd.isna(annotation):
- annotation = str(annotation).upper()
+ # setting readonly to true based on annotation and field type
+ if row.get("annotation"):
+ annotation = row.get("annotation").upper()
if (
"@READONLY" in annotation
or "@HIDDEN" in annotation
or "@CALCTEXT" in annotation
- or field_type in COMPUTE_LIST
):
- ui_obj["readonlyValue"] = True
-
- rowData["ui"] = ui_obj
- rowData["responseOptions"] = {"valueType": [value_type]}
-
- # Handle specific field type configurations
- if field_type == "yesno":
- rowData["responseOptions"]["choices"] = [
- {"name": {"en": "Yes"}, "value": 1},
- {"name": {"en": "No"}, "value": 0},
- ]
- elif field_type == "checkbox":
- rowData["responseOptions"]["multipleChoice"] = True
-
- for key, value in field.items():
- if pd.isna(value):
- continue
- schema_key = SCHEMA_MAP.get(key)
- if not schema_key:
- continue
-
- if schema_key in ["question", "description"]:
- parsed_value = parse_html(value)
- if parsed_value:
- rowData[schema_key] = parsed_value
-
- elif schema_key == "preamble" and add_preamble:
- parsed_value = parse_html(value)
- if parsed_value:
- rowData[schema_key] = parsed_value
-
- elif schema_key == "allow":
- ui_obj["allow"] = value.split(", ")
-
- # choices are only for some input_types
- elif schema_key == "choices" and input_type in [
- "radio",
- "select",
- "slider",
- ]:
- choices, choices_val_type_l = process_choices(
- value, field_name=field["Variable / Field Name"]
- )
- if choices is not None:
- if input_type == "slider":
- rowData["responseOptions"].update(
- {
- "choices": choices,
- "valueType": choices_val_type_l,
- "minValue": 0,
- "maxValue": 100,
- }
- )
- else:
- rowData["responseOptions"].update(
- {
- "choices": choices,
- "valueType": choices_val_type_l,
- }
- )
- # for now adding only for numerics, sometimes can be string or date.. TODO
- elif schema_key in RESPONSE_COND and value_type in [
- "xsd:integer",
- "xsd:decimal",
- ]:
- try:
- if value_type == "xsd:integer":
- parsed_value = int(value)
- else:
- parsed_value = float(value)
- rowData["responseOptions"][schema_key] = parsed_value
- except ValueError:
- print(f"Warning: Value {value} is not a valid {value_type}")
- continue
-
- # elif key == "Identifier?" and value:
- # identifier_val = value.lower() == "y"
- # rowData.update(
- # {
- # schema_map[key]: [
- # {"legalStandard": "unknown", "isIdentifier": identifier_val}
- # ]
- # }
- # )
-
- elif key in ADDITIONAL_NOTES_LIST:
- value_str = str(value).strip()
- if value_str:
- notes_obj = {
- "source": "redcap",
- "column": key,
- "value": f'"{value_str}"',
- }
- rowData.setdefault("additionalNotesObj", []).append(notes_obj)
-
- cleaned_data = clean_dict_nans(rowData)
- if not cleaned_data or "id" not in cleaned_data:
- raise ValueError(f"Missing required fields for item {item_id}")
+ item_data["ui"]["readonlyValue"] = True
+ elif input_type_rc in COMPUTE_LIST + ["descriptive"]:
+ item_data["ui"]["readonlyValue"] = True
+
+ # adding information from all "unprocessed" columns to the additionalNotesObj
+ for key_orig in ADDITIONAL_NOTES_LIST:
+ key = REDCAP_COLUMN_MAP.get(key_orig)
+ if row.get(key) and str(row.get(key)).strip():
+ notes_obj = {
+ "source": "redcap",
+ "column": key_orig,
+ "value": str(row.get(key)).strip(),
+ }
+ item_data.setdefault("additionalNotesObj", []).append(notes_obj)
- it = Item(**rowData)
- file_path_item = os.path.join(
- f"{abs_folder_path}",
- "activities",
- form_name,
- "items",
- item_id,
+ # processing preamble
+ item_preamble, preamble_info_propagate = process_preamble(
+ row, prior_preamble_info, input_type_rc
)
-
- write_obj_jsonld(it, file_path_item, contextfile_url=schema_context_url)
-
-
-# create activity
-def create_form_schema(
- abs_folder_path,
- schema_context_url,
- redcap_version,
- form_name,
- activity_display_name,
- order,
- bl_list,
- matrix_list,
- compute_list,
- preamble=None,
-):
- """
- Create the JSON-LD schema for an Activity.
-
- Args:
- abs_folder_path (str/Path): Path to the output directory
- schema_context_url (str): URL for the schema context
- redcap_version (str): Version of REDCap being used
- form_name (str): Name of the form
- activity_display_name (str): Display name for the activity
- order (list): List of items in order
- bl_list (list): List of branching logic properties
- matrix_list (list): List of matrix group properties
- compute_list (list): List of computation fields
- preamble (str, optional): Form preamble text
- """
- try:
- # Validate inputs
- if (
- pd.isna(form_name).any()
- if isinstance(form_name, pd.Series)
- else pd.isna(form_name)
- ):
- raise ValueError("Form name is required")
-
- # Set default activity display name if not provided
- if (
- pd.isna(activity_display_name).any()
- if isinstance(activity_display_name, pd.Series)
- else pd.isna(activity_display_name)
- ):
- activity_display_name = str(form_name).replace("_", " ").title()
-
- # Clean and validate order list
- clean_order = []
- if order is not None:
- if isinstance(order, (list, pd.Series, np.ndarray)):
- clean_order = [
- str(item).strip()
- for item in order
- if not (isinstance(item, pd.Series) and item.isna().any())
- and not pd.isna(item)
- ]
- clean_order = list(dict.fromkeys(clean_order))
-
- # Clean and validate bl_list
- clean_bl_list = []
- if bl_list is not None:
- if isinstance(bl_list, (list, pd.Series, np.ndarray)):
- clean_bl_list = [
- prop
- for prop in bl_list
- if prop is not None and isinstance(prop, dict)
- ]
-
- # Initialize schema
- json_ld = {
- "category": "reproschema:Activity",
- "id": f"{form_name}_schema",
- "prefLabel": {"en": str(activity_display_name)},
- "schemaVersion": get_context_version(schema_context_url),
- "version": redcap_version,
- "ui": {
- "order": clean_order,
- "addProperties": clean_bl_list,
- "shuffle": False,
- },
- }
-
- # Process preamble if present
- if preamble is not None:
- if isinstance(preamble, pd.Series):
- if not preamble.isna().all():
- parsed_preamble = parse_html(
- preamble.iloc[0] if len(preamble) > 0 else None
- )
- if parsed_preamble:
- json_ld["preamble"] = parsed_preamble
- elif not pd.isna(preamble):
- parsed_preamble = parse_html(preamble)
- if parsed_preamble:
- json_ld["preamble"] = parsed_preamble
-
- # Process matrix info if present
- if matrix_list and len(matrix_list) > 0:
- json_ld["matrixInfo"] = matrix_list
-
- # Process compute list if present
- if compute_list and len(compute_list) > 0:
- json_ld["compute"] = compute_list
-
- # Create Activity object and write to file
- act = Activity(**json_ld)
- path = Path(abs_folder_path) / "activities" / str(form_name)
- path.mkdir(parents=True, exist_ok=True)
-
- write_obj_jsonld(
- act,
- path / f"{form_name}_schema",
- contextfile_url=schema_context_url,
- )
-
- except Exception as e:
- raise Exception(
- f"Error creating form schema for {form_name}: {str(e)}"
+ if item_preamble:
+ item_data["preamble"] = item_preamble
+
+ # processing information needed for the activity schema
+ # checking compute
+ compute = None
+ if input_type_rc in COMPUTE_LIST:
+ condition = normalize_condition(row.get("choices"))
+ compute = {"variableName": row["item_name"], "jsExpression": condition}
+ elif (
+ row.get("annotation") and "@CALCTEXT" in row.get("annotation").upper()
+ ):
+ calc_text = row.get("annotation")
+ match = re.search(r"@CALCTEXT\((.*)\)", normalize_condition(calc_text))
+ if match:
+ js_expression = match.group(1)
+ compute = {
+ "variableName": row["item_name"],
+ "jsExpression": js_expression,
+ }
+ else:
+ print(
+ f"Warning/Error: Invalid @CALCTEXT annotation in {row['item_name']}: {calc_text}"
+ )
+ # for compute items, we should use description instead of question
+ if compute:
+ item_data["description"] = item_data.pop("question")
+
+ # setting default properties
+ addProperties = {
+ "variableName": item_data["id"],
+ "isAbout": f"items/{item_data['id']}",
+ "valueRequired": False,
+ "isVis": True,
+ }
+ if row.get("valueRequired") and str(
+ row.get("valueRequired")
+ ).strip().lower() in ["y", "yes", "true"]:
+ addProperties["valueRequired"] = True
+ elif row.get("valueRequired") and str(
+ row.get("valueRequired")
+ ).strip().lower() not in ["n", "no", "false"]:
+ print(
+ f"Warning: Unexpected value for valueRequired in {row['item_name']}: {row.get('valueRequired')}"
)
+ if row.get("annotation") and (
+ "@READONLY" in row.get("annotation").upper()
+ or "@HIDDEN" in row.get("annotation").upper()
+ ):
+ addProperties["isVis"] = False
+ elif compute:
+ addProperties["isVis"] = False
+ elif row.get("visibility"):
+ addProperties["isVis"] = normalize_condition(row.get("visibility"))
-def process_activities(activity_name, protocol_visibility_obj, protocol_order):
- # Set default visibility condition
- protocol_visibility_obj[activity_name] = True
-
- protocol_order.append(activity_name)
-
-
-def create_protocol_schema(
- abs_folder_path,
- schema_context_url,
- redcap_version,
- protocol_name,
- protocol_display_name,
- protocol_description,
- protocol_order,
- protocol_visibility_obj,
-):
- # Construct the protocol schema
- protocol_schema = {
- "category": "reproschema:Protocol",
- "id": f"{protocol_name}_schema",
- "prefLabel": {"en": protocol_display_name},
- # "altLabel": {"en": f"{protocol_name}_schema"}, todo: should we add this?
- "description": {"en": protocol_description},
- "schemaVersion": "1.0.0-rc4",
- "version": redcap_version,
- "ui": {
- "addProperties": [],
- "order": [],
- "shuffle": False,
- },
- }
+ return item_data, preamble_info_propagate, compute, addProperties
- # Populate addProperties list
- for activity in protocol_order:
- full_path = f"../activities/{activity}/{activity}_schema"
- add_property = {
- "isAbout": full_path,
- "variableName": f"{activity}_schema",
- # Assuming activity name as prefLabel, update as needed
- "prefLabel": {"en": activity.replace("_", " ").title()},
- "isVis": protocol_visibility_obj.get(
- activity, True
- ), # Default to True if not specified
- }
- protocol_schema["ui"]["addProperties"].append(add_property)
- # Add the full path to the order list
- protocol_schema["ui"]["order"].append(full_path)
- prot = Protocol(**protocol_schema)
- # Write the protocol schema to file
- protocol_dir = f"{abs_folder_path}/{protocol_name}"
- os.makedirs(protocol_dir, exist_ok=True)
- schema_file = f"{protocol_name}_schema"
- file_path = os.path.join(protocol_dir, schema_file)
- write_obj_jsonld(prot, file_path, contextfile_url=schema_context_url)
- print(f"Protocol schema created in {file_path}")
+def process_csv(csv_file) -> (Dict[str, Any], list):
+ df = pd.read_csv(
+ csv_file, encoding="utf-8-sig", low_memory=False
+ ) # utf-8-sig handles BOM automatically
-def process_csv(csv_file, abs_folder_path, protocol_name):
- datas = {}
- order = {}
- compute = {}
+ df.columns = df.columns.map(
+ lambda x: x.strip().strip('"')
+ ) # some cleaning might not be needed
- # TODO: add languages
+ # Clean NaNs values in the dataframe
+ df = df.astype(str).replace("nan", "")
- try:
- df = pd.read_csv(csv_file, encoding="utf-8-sig")
- df.columns = df.columns.map(
- lambda x: x.strip().strip('"').lstrip("\ufeff")
+ # Validate required columns
+ missing_columns = set(REDCAP_COLUMN_REQUIRED) - set(df.columns)
+ if missing_columns:
+ raise ValueError(
+ f"Missing required columns: {', '.join(missing_columns)}"
+ )
+ different_columns = set(df.columns) - set(REDCAP_COLUMN_MAP.keys())
+ if different_columns:
+ print(
+ "Warning: Found columns that are not in the mapping: ",
+ different_columns,
)
- required_columns = ["Form Name", "Variable / Field Name", "Field Type"]
- missing_columns = [
- col for col in required_columns if col not in df.columns
- ]
- if missing_columns:
- raise ValueError(
- f"Missing required columns: {', '.join(missing_columns)}"
- )
-
- # Initialize structures for each unique form
- unique_forms = df["Form Name"].dropna().unique()
- if len(unique_forms) == 0:
- raise ValueError("No valid form names found in the CSV")
-
- for form_name in unique_forms:
- form_name = str(form_name).strip()
- if not form_name:
- continue
-
- datas[form_name] = []
- order[form_name] = []
- compute[form_name] = []
-
- form_dir = (
- Path(abs_folder_path) / "activities" / form_name / "items"
+ df = df.rename(columns=REDCAP_COLUMN_MAP)
+ activities = {}
+ prot_actvities_order = []
+ for activity_name, group in df.groupby("activity_name", sort=False):
+ if not activity_name:
+ print("WARNING: Some rows in CSV have no activity name, skipping")
+ continue
+ items = []
+ item_preamble_info = None
+ act_addProperties = []
+ act_items_order = []
+ act_compute = []
+ act_preamble = []
+ for row in group.to_dict("records"):
+ item, item_preamble_info, compute, addProperty = process_row(
+ row, prior_preamble_info=item_preamble_info
)
- form_dir.mkdir(parents=True, exist_ok=True)
-
- # TODO: should we bring back the language
- # if not languages:
- # languages = parse_language_iso_codes(row["Field Label"])
-
- for idx, row in df.iterrows():
- form_name = row["Form Name"]
- field_name = row["Variable / Field Name"]
-
- # Skip rows with missing essential data
- if pd.isna(form_name) or pd.isna(field_name):
- print(
- f"Warning: Skipping row {idx+2} with missing form name or field name"
- )
- continue
-
- form_name = str(form_name).strip()
- field_name = str(field_name).strip()
-
- # Convert row to dict and clean NaN values
- row_dict = {k: v for k, v in row.to_dict().items() if pd.notna(v)}
- if not row_dict:
- print(f"Warning: Skipping empty row {idx+2}")
- continue
-
- datas[form_name].append(row_dict)
- field_path = f"items/{field_name}"
-
- field_type = row_dict.get("Field Type", "").strip().lower()
- field_annotation = row_dict.get("Field Annotation", "")
-
- # Handle compute fields
- is_compute = False
-
- # Case 1: Field is calc type
- if field_type in COMPUTE_LIST:
- calc_value = row_dict.get(
- "Choices, Calculations, OR Slider Labels", ""
- )
- if calc_value and str(calc_value).strip():
- compute_expression = normalize_condition(
- calc_value, field_type=field_type
- )
- if compute_expression:
- is_compute = True
- compute[form_name].append(
- {
- "variableName": field_name,
- "jsExpression": compute_expression,
- }
- )
- else:
- print(
- f"Warning: Could not normalize calc expression for {field_name}: {calc_value}"
- )
-
- # Case 2: Field has @CALCTEXT
- elif (
- field_annotation
- and "@CALCTEXT" in str(field_annotation).upper()
- ):
- match = re.search(r"@CALCTEXT\((.*)\)", field_annotation)
- if match:
- compute_expression = normalize_condition(match.group(1))
- if compute_expression:
- is_compute = True
- compute[form_name].append(
- {
- "variableName": field_name,
- "jsExpression": compute_expression,
- }
- )
-
- # Add to order list only if not a compute field
- if not is_compute:
- order[form_name].append(field_path)
-
- return datas, order, compute
+ items.append(item)
+ act_addProperties.append(addProperty)
+ if compute:
+ act_compute.append(compute)
+ else:
+ act_items_order.append(f"items/{item['id']}")
+ if item.get("preamble"):
+ act_preamble.append(item["preamble"]["en"])
+
+ activities[activity_name] = {
+ "items": items,
+ "order": act_items_order,
+ "compute": act_compute,
+ "addProperties": act_addProperties,
+ }
+ prot_actvities_order.append(activity_name)
+ # checking if all preamble the same for all questions
+ # if they are, it should be treated as an activity preamble
+ act_compute_name = [c["variableName"] for c in act_compute]
+ if (
+ act_preamble
+ and len(set(act_preamble)) == 1
+ and len(act_preamble) == len(act_items_order)
+ ):
+ activities[activity_name]["preamble"] = {"en": act_preamble[0]}
+ for item in items:
+ # I was checking only for questions to see if this can be treated as an activity preamble,
+ # but if there is a preamble also for compute item it should be removed
+ if item["id"] in act_compute_name:
+ if item.get("preamble") == {"en": act_preamble[0]}:
+ del item["preamble"]
+ else:
+ del item["preamble"]
- except Exception as e:
- print(f"Error processing CSV: {str(e)}")
- raise
+ return activities, prot_actvities_order
-# todo adding output path
def redcap2reproschema(
csv_file, yaml_file, output_path, schema_context_url=None
):
@@ -949,173 +512,41 @@ def redcap2reproschema(
FileNotFoundError: If input files cannot be found
Exception: For other processing errors
"""
- try:
- # Validate input files exist
- csv_path = Path(csv_file)
- yaml_path = Path(yaml_file)
- output_dir = Path(output_path)
-
- if not csv_path.exists():
- raise FileNotFoundError(f"CSV file not found: {csv_file}")
- if not yaml_path.exists():
- raise FileNotFoundError(f"YAML file not found: {yaml_file}")
-
- # Read and validate YAML configuration
- try:
- with open(yaml_path, "r", encoding="utf-8") as f:
- protocol = yaml.safe_load(f)
- except yaml.YAMLError as e:
- raise ValueError(f"Invalid YAML file: {str(e)}")
-
- # Extract and validate protocol information
- protocol_name = protocol.get("protocol_name", "").strip()
- if not protocol_name:
- raise ValueError("Protocol name not specified in the YAML file")
-
- protocol_display_name = protocol.get(
- "protocol_display_name", protocol_name
- )
- protocol_description = protocol.get("protocol_description", "")
- redcap_version = protocol.get("redcap_version", "1.0.0")
- # Set up output directory
- protocol_name = protocol_name.replace(" ", "_")
- abs_folder_path = output_dir / protocol_name
- abs_folder_path.mkdir(parents=True, exist_ok=True)
-
- # Set schema context URL
- if schema_context_url is None:
- schema_context_url = CONTEXTFILE_URL
-
- # Process CSV file
- print(f"Processing CSV file: {csv_path}")
- datas, order, compute = process_csv(
- csv_path, abs_folder_path, protocol_name
- )
-
- if not datas:
- raise ValueError("No valid data found in CSV file")
-
- # Initialize protocol variables
- protocol_visibility_obj = {}
- protocol_order = []
-
- # Process each form
- for form_name, rows in datas.items():
- print(f"\nProcessing form: {form_name}")
- if not rows:
- print(f"Warning: Empty form {form_name}, skipping")
- continue
-
- # Initialize form-level collections
- bl_list = []
- matrix_list = []
- preambles_list = []
-
- # Process fields in the form
- for field in rows:
- # Validate field data
- if (
- not isinstance(field, dict)
- or "Variable / Field Name" not in field
- ):
- print(
- f"Warning: Invalid field data in form {form_name}, skipping"
- )
- continue
-
- # Process field properties
- field_properties = process_field_properties(field)
- if field_properties:
- bl_list.append(field_properties)
-
- # Handle matrix groups
- matrix_group = field.get("Matrix Group Name")
- matrix_ranking = field.get("Matrix Ranking?")
- if pd.notna(matrix_group) or pd.notna(matrix_ranking):
- matrix_info = {
- "variableName": field["Variable / Field Name"],
- }
- if pd.notna(matrix_group):
- matrix_info["matrixGroupName"] = matrix_group
- if pd.notna(matrix_ranking):
- matrix_info["matrixRanking"] = matrix_ranking
- matrix_list.append(matrix_info)
-
- # Handle preambles (section headers)
- preamble = field.get("Section Header")
- if pd.notna(preamble):
- preamble = str(preamble).strip()
- if preamble:
- preambles_list.append(preamble)
-
- # Determine preamble handling strategy
- unique_preambles = set(preambles_list)
- if len(unique_preambles) == 1:
- # Single preamble for the whole form
- preamble_act = preambles_list[0]
- preamble_itm = False
- elif len(unique_preambles) == 0:
- # No preambles
- preamble_act = None
- preamble_itm = False
- else:
- # Multiple preambles, handle at item level
- preamble_act = None
- preamble_itm = True
-
- # Get form display name
- activity_display_name = rows[0].get("Form Name", form_name)
-
- # Create form schema
- print(f"Creating schema for form: {form_name}")
- create_form_schema(
- abs_folder_path=abs_folder_path,
- schema_context_url=schema_context_url,
- redcap_version=redcap_version,
- form_name=form_name,
- activity_display_name=activity_display_name,
- order=order[form_name],
- bl_list=bl_list,
- matrix_list=matrix_list,
- compute_list=compute[form_name],
- preamble=preamble_act, # Note: using correct parameter name
- )
-
- # Process individual items
- for field in rows:
- field_name = field["Variable / Field Name"]
- print(f"Processing field: {field_name}")
- process_row(
- abs_folder_path=abs_folder_path,
- schema_context_url=schema_context_url,
- form_name=form_name,
- field=field,
- add_preamble=preamble_itm, # Note: consistent parameter naming
- )
-
- # Process form-level activities
- print(f"Processing activities for form: {form_name}")
- process_activities(
- form_name, protocol_visibility_obj, protocol_order
- )
-
- # Create final protocol schema
- print("\nCreating protocol schema")
- create_protocol_schema(
- abs_folder_path=abs_folder_path,
- schema_context_url=schema_context_url,
- redcap_version=redcap_version,
- protocol_name=protocol_name,
- protocol_display_name=protocol_display_name,
- protocol_description=protocol_description,
- protocol_order=protocol_order,
- protocol_visibility_obj=protocol_visibility_obj,
+ # Validate input files exist
+ csv_path = Path(csv_file)
+ yaml_path = Path(yaml_file)
+ output_dir = Path(output_path)
+
+ if not csv_path.exists():
+ raise FileNotFoundError(f"CSV file not found: {csv_file}")
+ if not yaml_path.exists():
+ raise FileNotFoundError(f"YAML file not found: {yaml_file}")
+
+ protocol = read_check_yaml_config(yaml_path)
+ protocol_name = protocol.get("protocol_name").replace(" ", "_")
+ # Set up output directory
+ abs_folder_path = output_dir / protocol_name
+ abs_folder_path.mkdir(parents=True, exist_ok=True)
+
+ # Set schema context URL
+ if schema_context_url is None:
+ schema_context_url = CONTEXTFILE_URL
+
+ # Process the CSV file and getting information about the activities and items
+ activities, prot_activities_order = process_csv(csv_path)
+
+ for activity_name, activity_data in activities.items():
+ create_activity_schema(
+ activity_name,
+ activity_data,
+ abs_folder_path,
+ protocol.get("redcap_version"),
+ schema_context_url,
)
- print(
- f"\nConversion completed successfully. Output directory: {abs_folder_path}"
- )
-
- except Exception as e:
- raise Exception(f"Error during conversion: {str(e)}") from e
+ # Create protocol schema
+ create_protocol_schema(
+ protocol, prot_activities_order, abs_folder_path, schema_context_url
+ )
+ print("OUTPUT DIRECTORY: ", abs_folder_path)
diff --git a/reproschema/redcap_mappings.py b/reproschema/redcap_mappings.py
new file mode 100644
index 0000000..9ff2066
--- /dev/null
+++ b/reproschema/redcap_mappings.py
@@ -0,0 +1,107 @@
+# All the mapping used in the code
+REDCAP_COLUMN_MAP = {
+ "Variable / Field Name": "item_name", # column A
+ "Form Name": "activity_name", # column B
+ "Section Header": "preamble", # column C
+ "Field Type": "inputType", # column D
+ "Field Label": "question", # column E
+ "Choices, Calculations, OR Slider Labels": "choices", # column F
+ "Field Note": "note", # column G
+ "Text Validation Type OR Show Slider Number": "validation", # column H
+ "Text Validation Min": "minValue", # column I
+ "Text Validation Max": "maxValue", # column J
+ "Identifier?": "identifiable", # column K
+ "Branching Logic (Show field only if...)": "visibility", # column L
+ "Required Field?": "valueRequired", # column M
+ "Custom Alignment": "customAlignment", # column N
+ "Question Number (surveys only)": "questionNumber", # column O
+ "Matrix Group Name": "matrixGroup", # column P
+ "Matrix Ranking?": "matrixRanking", # column Q
+ "Field Annotation": "annotation", # column R
+}
+REDCAP_COLUMN_MAP_REVERSE = {v: k for k, v in REDCAP_COLUMN_MAP.items()}
+
+REDCAP_COLUMN_REQUIRED = [
+ "Variable / Field Name",
+ "Form Name",
+ "Field Type",
+ "Field Label",
+ "Choices, Calculations, OR Slider Labels",
+]
+
+INPUT_TYPE_MAP = {
+ "calc": "number",
+ "sql": "number",
+ "yesno": "radio",
+ "radio": "radio",
+ "truefalse": "radio",
+ "checkbox": "radio",
+ "descriptive": "static",
+ "dropdown": "select",
+ "text": "text",
+ "notes": "text",
+ "file": "documentUpload",
+ "slider": "slider",
+}
+
+# Map certain field types directly to xsd types
+VALUE_TYPE_MAP = {
+ # Basic types
+ "text": "xsd:string",
+ "email": "xsd:string",
+ "phone": "xsd:string",
+ "signature": "xsd:string",
+ "zipcode": "xsd:string",
+ "autocomplete": "xsd:string",
+ # Numeric types
+ "number": "xsd:decimal", # This includes both integer and float, redcap use for both
+ "float": "xsd:decimal",
+ "integer": "xsd:integer",
+ # Date and time types will be handled by pattern matching in process_input_value_types
+ # These entries are kept for backward compatibility
+ "date_": "xsd:date",
+ "time_": "xsd:time",
+}
+
+# field types that should be used as compute
+COMPUTE_LIST = ["calc", "sql"]
+RESPONSE_COND = ["minValue", "maxValue"]
+ADDITIONAL_NOTES_LIST = [
+ "Field Note",
+ "Question Number (surveys only)",
+ "Matrix Group Name",
+ "Matrix Ranking?",
+ "Text Validation Type OR Show Slider Number",
+ "Text Validation Min",
+ "Text Validation Max",
+ "Identifier?",
+ "Custom Alignment",
+ "Question Number (surveys only)",
+ "Field Annotation",
+]
+
+
+def get_value_type(validation_type):
+ """
+ Determine the XSD value type based on REDCap validation type
+
+ Args:
+ validation_type (str): Validation type from REDCap
+
+ Returns:
+ str: XSD value type for ReproSchema
+ """
+ # Handle date and time formats with pattern matching
+ if validation_type.startswith("date_"):
+ return "xsd:date"
+ elif validation_type.startswith("datetime_"):
+ return "xsd:dateTime"
+ elif validation_type.startswith("time"):
+ return "xsd:time"
+ elif validation_type in VALUE_TYPE_MAP:
+ return VALUE_TYPE_MAP[validation_type]
+ else:
+ raise ValueError(
+ f"Validation type: {validation_type} is not supported yet. "
+ "Please add it to VALUE_TYPE_MAP."
+ )
diff --git a/reproschema/reproschema2redcap.py b/reproschema/reproschema2redcap.py
index 6f604c4..4ffc86d 100644
--- a/reproschema/reproschema2redcap.py
+++ b/reproschema/reproschema2redcap.py
@@ -7,6 +7,7 @@
from .context_url import CONTEXTFILE_URL
from .jsonldutils import _is_url, load_file
from .models import Activity, Item, Protocol, ResponseOption
+from .redcap_mappings import REDCAP_COLUMN_MAP, REDCAP_COLUMN_MAP_REVERSE
from .utils import start_server, stop_server
logger = logging.getLogger(__name__)
@@ -39,64 +40,52 @@ def fetch_choices_from_url(url):
return ""
-def find_Ftype_and_colH(item, row_data, response_options):
+def find_input_type_value_type_rc(item, response_options):
"""
- Determine field type and column H value.
+ Determine input type and value type that should be in RedCap
Args:
item: Item object containing UI information
- row_data: Dictionary to store field data
response_options: Response options object
Returns:
dict: Updated row_data with field type and validation info
"""
# Extract the input type from the item_json
- f_type = item.ui.inputType
- col_h = ""
-
- if f_type in ["text", "textarea", "email"]:
- f_type = "text"
- elif f_type in ["static", "save"]:
- f_type = "descriptive"
- elif f_type == "integer":
- f_type = "text"
- col_h = "integer"
- elif f_type == "number":
- f_type = "text"
- col_h = "integer"
- elif f_type == "float":
- f_type = "text"
- col_h = "float"
- elif f_type == "date":
- f_type = "text"
- col_h = "date_mdy"
- elif f_type == "select":
- multiple_choice = getattr(response_options, "multipleChoice", False)
- logger.debug(
- f"Multiple choice setting for {item.id}: {multiple_choice}"
- )
- f_type = "checkbox" if multiple_choice else "dropdown"
- elif f_type == "radio":
+ input_type = item.ui.inputType
+ value_type_rc = ""
+
+ if "text" in input_type:
+ input_type_rc = "text"
+ elif input_type in ["static", "save"]:
+ input_type_rc = "descriptive"
+ elif input_type == "number":
+ input_type_rc = "text"
+ value_type_rc = "integer"
+ elif input_type == "float":
+ input_type_rc = "text"
+ value_type_rc = "float"
+ elif input_type == "date":
+ input_type_rc = "text"
+ value_type_rc = "date_mdy" # TODO: redcap has more types
+ elif input_type.startswith("select"):
+ input_type_rc = "dropdown"
+ elif input_type == "radio":
if getattr(response_options, "multipleChoice", False):
- f_type = "checkbox"
- elif f_type.startswith("select"):
- f_type = "radio"
- choices_url = getattr(response_options, "choices", None)
- if choices_url and isinstance(choices_url, str):
- choices_data = fetch_choices_from_url(choices_url)
- if choices_data:
- row_data["choices"] = choices_data
- elif f_type.startswith(("audio", "video", "image", "document")):
- f_type = "file"
+ input_type_rc = "checkbox"
+ else:
+ input_type_rc = "radio" # todo: should add yes, no?
+ elif input_type.startswith(("audio", "video", "image", "document")):
+ input_type_rc = "file"
else:
- f_type = "text"
+ print(f"Warning: Unknown input type: {input_type}, defaulting to text")
+ input_type_rc = "text"
- row_data["field_type"] = f_type.lower()
- if col_h:
- row_data["val_type_OR_slider"] = col_h.lower()
+ info_rc = {"inputType": input_type_rc.lower()}
+ if value_type_rc:
+ info_rc["validation"] = value_type_rc.lower()
- return row_data
+ return info_rc
def process_item(
@@ -106,7 +95,6 @@ def process_item(
activity_preamble,
contextfile,
http_kwargs,
- compute_item=False,
compute_expr=None,
):
"""
@@ -145,14 +133,18 @@ def process_item(
# Only add values if they exist
if response_options:
if response_options.minValue is not None:
- row_data["val_min"] = response_options.minValue
+ row_data["minValue"] = response_options.minValue
if response_options.maxValue is not None:
- row_data["val_max"] = response_options.maxValue
+ row_data["maxValue"] = response_options.maxValue
# Handle choices
choices = response_options.choices
- if choices and not isinstance(choices, str):
- if isinstance(choices, list):
+ if choices:
+ if isinstance(choices, str):
+ choices_data = fetch_choices_from_url(choices)
+ if choices_data:
+ row_data["choices"] = choices_data
+ elif isinstance(choices, list):
# Handle the case where choices is a list
item_choices = []
for ch in choices:
@@ -165,6 +157,10 @@ def process_item(
item_choices.append(f"{ch.value}, {name}")
if item_choices:
row_data["choices"] = " | ".join(item_choices)
+ else:
+ raise Exception(
+ f"Choices should be a string or list, got {choices}"
+ )
# Add valueRequired if explicitly True
if (
@@ -172,45 +168,30 @@ def process_item(
and isinstance(item_properties, dict) # Ensure it's a dictionary
and item_properties.get("valueRequired") is True
):
- row_data["required"] = "y"
+ row_data["valueRequired"] = "y"
var_name = str(item.id).split("/")[-1] # Get the last part of the id path
# Handle compute items
- if compute_item and compute_expr:
+ if compute_expr:
logger.debug(f"Processing compute item: {var_name}")
logger.debug(f"Compute expression: {compute_expr}")
row_data["choices"] = compute_expr
- row_data["field_type"] = "calc"
- # For computed fields, we may need to set visibility to false by default
- if any(score_type in var_name for score_type in ["_score", "_total"]):
- row_data["isVis_logic"] = False
+ row_data["inputType"] = "calc" # todo: we don't have sql
+ row_data["visibility"] = False
else:
- # Use find_Ftype_and_colH but only add non-empty values
- field_info = find_Ftype_and_colH(item, {}, response_options)
- if field_info.get("field_type"):
- row_data["field_type"] = field_info["field_type"]
- if field_info.get("val_type_OR_slider"):
- row_data["val_type_OR_slider"] = field_info["val_type_OR_slider"]
-
- # Handle visibility
- if var_name.endswith("_total_score"):
- row_data["isVis_logic"] = False
- elif (
+ field_info = find_input_type_value_type_rc(item, response_options)
+ row_data["inputType"] = field_info["inputType"]
+ if field_info.get("validation"):
+ row_data["validation"] = field_info["validation"]
+
+ if (
item_properties
and isinstance(item_properties, dict) # Ensure it's a dictionary
and "isVis" in item_properties
and item_properties["isVis"] is not True
):
- row_data["isVis_logic"] = item_properties["isVis"]
-
- # Handle description
- if (
- hasattr(item, "description")
- and isinstance(item.description, dict)
- and item.description.get("en")
- ):
- row_data["field_notes"] = item.description["en"]
+ row_data["visibility"] = item_properties["isVis"]
# Handle preamble
if (
@@ -223,15 +204,15 @@ def process_item(
row_data["preamble"] = activity_preamble
# Handle question/field label
- if compute_item:
+ if compute_expr:
question = item.description
else:
question = item.question if hasattr(item, "question") else None
if isinstance(question, dict) and question.get("en"):
- row_data["field_label"] = question["en"]
+ row_data["question"] = question["en"]
elif isinstance(question, str) and question:
- row_data["field_label"] = question
+ row_data["question"] = question
return row_data
@@ -259,115 +240,88 @@ def get_csv_data(dir_path, contextfile, http_kwargs):
for activity_path in activity_order:
if not _is_url(activity_path):
activity_path = protocol_dir / activity_path
-
- parsed_activity_json = load_file(
- activity_path,
- started=True,
- http_kwargs=http_kwargs,
- fixoldschema=True,
- compact=True,
- compact_context=contextfile,
+ act_data = process_activity(
+ activity_path, contextfile, http_kwargs
)
- del parsed_activity_json["@context"]
- act = Activity(**parsed_activity_json)
-
- # Get activity name
- activity_name = act.id.split("/")[-1]
- if activity_name.endswith("_schema.jsonld"):
- activity_name = activity_name[:-12]
- elif activity_name.endswith(".jsonld"):
- activity_name = activity_name[:-7]
-
- # Create a map of computed items
- compute_map = {}
- if hasattr(act, "compute"):
- compute_map = {
- comp.variableName: comp.jsExpression
- for comp in act.compute
- }
-
- # Process each item defined in addProperties
- for item_def in parsed_activity_json["ui"][
- "addProperties"
- ]:
- item_path = item_def["isAbout"]
- var_name = item_def["variableName"]
-
- # Get the item file path
- if not _is_url(item_path):
- full_item_path = (
- Path(activity_path).parent / item_path
- )
- else:
- full_item_path = item_path
-
- try:
- item_json = load_file(
- full_item_path,
- started=True,
- http_kwargs=http_kwargs,
- fixoldschema=True,
- compact=True,
- compact_context=contextfile,
- )
- item_json.pop("@context", "")
- item = Item(**item_json)
+ csv_data += act_data
+ return csv_data
- activity_preamble = (
- act.preamble.get("en", "").strip()
- if hasattr(act, "preamble")
- else ""
- )
- # Check if this is a computed item
- compute_expr = compute_map.get(var_name)
- is_computed = compute_expr is not None
-
- row_data = process_item(
- item,
- item_def,
- activity_name,
- activity_preamble,
- contextfile,
- http_kwargs,
- is_computed,
- compute_expr,
- )
- csv_data.append(row_data)
+def process_activity(activity_path, contextfile, http_kwargs):
+ parsed_activity_json = load_file(
+ activity_path,
+ started=True,
+ http_kwargs=http_kwargs,
+ fixoldschema=True,
+ compact=True,
+ compact_context=contextfile,
+ )
+ del parsed_activity_json["@context"]
+ act = Activity(**parsed_activity_json)
+
+ # Get activity name
+ activity_name = act.id.split("/")[-1]
+ if activity_name.endswith("_schema.jsonld"):
+ activity_name = activity_name[:-12]
+ elif activity_name.endswith(".jsonld"):
+ activity_name = activity_name[:-7]
- except Exception as e:
- print(
- f"Error processing item {item_path} for activity {activity_name}"
- )
- print(f"Error details: {str(e)}")
- continue
+ # Create a map of computed items
+ compute_map = {}
+ if hasattr(act, "compute"):
+ compute_map = {
+ comp.variableName: comp.jsExpression for comp in act.compute
+ }
+ act_data = []
+ var_name_list = []
+ # Process each item defined in addProperties
+ for item_def in parsed_activity_json["ui"]["addProperties"]:
+ item_path = item_def["isAbout"]
+ var_name = item_def["variableName"]
+ if var_name in var_name_list:
+ continue
+ else:
+ var_name_list.append(var_name)
+ # Get the item file path
+ if not _is_url(item_path):
+ full_item_path = Path(activity_path).parent / item_path
+ else:
+ full_item_path = item_path
- return csv_data
+ item_json = load_file(
+ full_item_path,
+ started=True,
+ http_kwargs=http_kwargs,
+ fixoldschema=True,
+ compact=True,
+ compact_context=contextfile,
+ )
+ item_json.pop("@context", "")
+ item = Item(**item_json)
+ activity_preamble = (
+ act.preamble.get("en", "").strip()
+ if hasattr(act, "preamble")
+ else ""
+ )
+ # Check if this is a computed item
+ compute_expr = compute_map.get(var_name)
+
+ row_data = process_item(
+ item,
+ item_def,
+ activity_name,
+ activity_preamble,
+ contextfile,
+ http_kwargs,
+ compute_expr,
+ )
+ act_data.append(row_data)
+ return act_data
-def write_to_csv(csv_data, output_csv_filename):
- # REDCap-specific headers
- headers = [
- "Variable / Field Name",
- "Form Name",
- "Section Header",
- "Field Type",
- "Field Label",
- "Choices, Calculations, OR Slider Labels",
- "Field Note",
- "Text Validation Type OR Show Slider Number",
- "Text Validation Min",
- "Text Validation Max",
- "Identifier?",
- "Branching Logic (Show field only if...)",
- "Required Field?",
- "Custom Alignment",
- "Question Number (surveys only)",
- "Matrix Group Name",
- "Matrix Ranking?",
- "Field Annotation",
- ]
+def write_to_csv(csv_data, output_csv_filename):
+ headers = list(REDCAP_COLUMN_MAP.keys())
# Writing to the CSV file
with open(
output_csv_filename, "w", newline="", encoding="utf-8"
@@ -390,41 +344,24 @@ def write_to_csv(csv_data, output_csv_filename):
activity_name = activity_name[:-7]
redcap_row["Form Name"] = activity_name
- # Map remaining fields
- field_mappings = {
- "preamble": "Section Header",
- "field_type": "Field Type",
- "field_label": "Field Label",
- "choices": "Choices, Calculations, OR Slider Labels",
- "field_notes": "Field Note",
- "val_type_OR_slider": "Text Validation Type OR Show Slider Number",
- "val_min": "Text Validation Min",
- "val_max": "Text Validation Max",
- "required": "Required Field?",
- "isVis_logic": "Branching Logic (Show field only if...)",
- "field_annotation": "Field Annotation",
- "matrix_group": "Matrix Group Name",
- "matrix_ranking": "Matrix Ranking?",
- }
-
# Add mapped fields only if they exist and aren't empty
- for src_key, dest_key in field_mappings.items():
+ for src_key, dest_key in REDCAP_COLUMN_MAP_REVERSE.items():
if (
src_key in row
and row[src_key] is not None
and row[src_key] != ""
):
# Special handling for visibility logic
- if src_key == "isVis_logic":
+ if src_key == "visibility":
if (
row[src_key] is not True
): # Only add if not default True
redcap_row[dest_key] = row[src_key]
# Special handling for required field
- elif src_key == "required":
+ elif src_key == "valueRequired":
redcap_row[dest_key] = "y" if row[src_key] else "n"
# Special handling for field annotation
- elif src_key == "field_annotation":
+ elif src_key == "annotation":
current_annotation = redcap_row.get(dest_key, "")
if current_annotation:
redcap_row[dest_key] = (
diff --git a/reproschema/tests/test_field_property.py b/reproschema/tests/test_field_property.py
index c6233f9..8fe02d1 100644
--- a/reproschema/tests/test_field_property.py
+++ b/reproschema/tests/test_field_property.py
@@ -1,117 +1,157 @@
-import csv
-
import pytest
-from ..redcap2reproschema import process_field_properties
+from ..redcap2reproschema import process_row
+from ..redcap_mappings import REDCAP_COLUMN_MAP
-def test_process_field_properties_calctext():
- """Test different CALCTEXT annotations with realistic examples"""
- test_cases = [
- # Simple CALCTEXT
- {
- "input": {
- "Variable / Field Name": "test_var",
- "Required Field?": "",
- "Field Annotation": "@CALCTEXT",
- "Branching Logic (Show field only if...)": "",
+def update_keys(data):
+ """Update keys in the dictionary to match the expected keys in the reproschema"""
+ # Add default value for "Field Label" if it is not present
+ if "Field Label" not in data:
+ data["Field Label"] = "question"
+ # Update keys to match the expected keys in the reproschema
+ updated_data = {}
+ for key, value in data.items():
+ updated_data[REDCAP_COLUMN_MAP[key]] = value
+ return updated_data
+
+
+@pytest.mark.parametrize(
+ "field_data,expected",
+ [
+ # Test case 1: No branching logic or annotations
+ ({"Variable / Field Name": "test_field"}, True),
+ # Test case 2: With branching logic
+ (
+ {
+ "Variable / Field Name": "test_field",
+ "Branching Logic (Show field only if...)": "[age] > 18",
},
- "expected": {
- "variableName": "test_var",
- "isAbout": "items/test_var",
- "isVis": False,
+ "age > 18",
+ ),
+ # Test case 3: With @HIDDEN annotation
+ (
+ {
+ "Variable / Field Name": "test_field",
+ "Field Annotation": "@HIDDEN",
},
- },
- # Complex CALCTEXT with conditional logic
- {
- "input": {
+ False,
+ ),
+ # Test case 4: With both branching logic and @HIDDEN
+ (
+ {
+ "Variable / Field Name": "test_field",
+ "Branching Logic (Show field only if...)": "[age] > 18",
+ "Field Annotation": "@HIDDEN",
+ },
+ False,
+ ),
+ ],
+)
+def test_process_field_properties_visibility(field_data, expected):
+ # Test case 1: No branching logic or annotations
+ _, _, _, add_prop = process_row(update_keys(field_data))
+ if expected is True:
+ assert add_prop.get("isVis", True) is True # defaults is True
+ else:
+ assert add_prop.get("isVis") == expected
+
+
+@pytest.mark.parametrize(
+ "input,expected",
+ [
+ # CALCTEXT with conditional logic
+ (
+ {
"Variable / Field Name": "parkinsons_diagnosis",
"Required Field?": "",
"Field Annotation": "@CALCTEXT(if(([diagnosis_parkinsons_gsd_category_1(bradykinesia)] && ([diagnosis_parkinsons_gsd_category_1(tremor)] || [diagnosis_parkinsons_gsd_category_1(rigidity)])), 'Yes', 'No'))",
"Branching Logic (Show field only if...)": "[some_other_condition] = 1",
},
- "expected": {
+ {
"variableName": "parkinsons_diagnosis",
"isAbout": "items/parkinsons_diagnosis",
"isVis": False,
},
- },
+ ),
# CALCTEXT with numerical operations
- {
- "input": {
+ (
+ {
"Variable / Field Name": "bmi",
"Required Field?": "",
"Field Annotation": "@CALCTEXT([weight]/([height]*[height]))",
"Branching Logic (Show field only if...)": "[weight] > 0 and [height] > 0",
},
- "expected": {
+ {
"variableName": "bmi",
"isAbout": "items/bmi",
"isVis": False,
},
- },
+ ),
# CALCTEXT with multiple nested conditions
- {
- "input": {
+ (
+ {
"Variable / Field Name": "complex_score",
"Required Field?": "",
"Field Annotation": "@CALCTEXT(if([score1] > 10 && [score2] < 5, 'High', if([score1] > 5, 'Medium', 'Low')))",
"Branching Logic (Show field only if...)": "",
},
- "expected": {
+ {
"variableName": "complex_score",
"isAbout": "items/complex_score",
"isVis": False,
},
- },
- ]
-
- for test_case in test_cases:
- result = process_field_properties(test_case["input"])
- for key, expected_value in test_case["expected"].items():
- assert (
- result[key] == expected_value
- ), f"Failed for {key} in test case with annotation: {test_case['input']['Field Annotation']}"
+ ),
+ ],
+)
+def test_process_field_properties_calctext(input, expected):
+ """Test different CALCTEXT annotations with realistic examples"""
+ _, _, _, add_prop = process_row(update_keys(input))
+ for key, expected_value in expected.items():
+ assert (
+ add_prop[key] == expected_value
+ ), f"Failed for {key} in test case with annotation: {input['Field Annotation']}"
-def test_process_field_properties_mixed_annotations():
- """Test fields with multiple annotations"""
- test_cases = [
+@pytest.mark.parametrize(
+ "input,expected",
+ [
# CALCTEXT with READONLY
- {
- "input": {
+ (
+ {
"Variable / Field Name": "test_var",
"Required Field?": "",
"Field Annotation": "@CALCTEXT @READONLY",
"Branching Logic (Show field only if...)": "",
},
- "expected": {"isVis": False},
- },
+ {"isVis": False},
+ ),
# CALCTEXT with HIDDEN
- {
- "input": {
+ (
+ {
"Variable / Field Name": "test_var",
"Required Field?": "",
"Field Annotation": "@HIDDEN @CALCTEXT(if([var1] > 0, 1, 0))",
"Branching Logic (Show field only if...)": "",
},
- "expected": {"isVis": False},
- },
+ {"isVis": False},
+ ),
# Complex CALCTEXT with other annotations
- {
- "input": {
+ (
+ {
"Variable / Field Name": "test_var",
"Required Field?": "",
"Field Annotation": "@CALCTEXT(if(([var1] && [var2]), 'Yes', 'No')) @READONLY @HIDDEN-SURVEY",
"Branching Logic (Show field only if...)": "[condition] = 1",
},
- "expected": {"isVis": False},
- },
- ]
-
- for test_case in test_cases:
- result = process_field_properties(test_case["input"])
- for key, expected_value in test_case["expected"].items():
- assert (
- result[key] == expected_value
- ), f"Failed for {key} in test case with annotation: {test_case['input']['Field Annotation']}"
+ {"isVis": False},
+ ),
+ ],
+)
+def test_process_field_properties_mixed_annotations(input, expected):
+ """Test fields with multiple annotations"""
+ _, _, _, add_prop = process_row(update_keys(input))
+ for key, expected_value in expected.items():
+ assert (
+ add_prop[key] == expected_value
+ ), f"Failed for {key} in test case with annotation: {input['Field Annotation']}"
diff --git a/reproschema/tests/test_process_csv.py b/reproschema/tests/test_process_csv.py
index f223e6b..e2b13aa 100644
--- a/reproschema/tests/test_process_csv.py
+++ b/reproschema/tests/test_process_csv.py
@@ -1,41 +1,42 @@
import tempfile
from pathlib import Path
-import pandas as pd
import pytest
-from ..redcap2reproschema import normalize_condition, process_csv
+from ..convertutils import normalize_condition
+from ..redcap2reproschema import process_csv
def test_process_csv():
- csv_data = """Form Name,Variable / Field Name,Field Type,Field Annotation,"Choices, Calculations, OR Slider Labels"
-form1,field1,text,,
-form1,field2,calc,,[field1] + [field3]
-form1,field3,text,@CALCTEXT(3*3),
-form2,field4,text,,
-,field5,text,,"""
+ csv_data = """Form Name,Variable / Field Name,Field Type,Field Label,Field Annotation,"Choices, Calculations, OR Slider Labels"
+form1,field1,text,,,
+form1,field2,calc,,,[field1]
+form1,field3,text,,@CALCTEXT(3*3),
+form2,field4,text,,,
+,field5,text,,,"""
with tempfile.TemporaryDirectory() as tmpdir:
csv_path = Path(tmpdir) / "test.csv"
csv_path.write_text(csv_data)
- datas, order, compute = process_csv(csv_path, tmpdir, "test_protocol")
+ datas, order = process_csv(csv_path)
assert set(datas.keys()) == {"form1", "form2"}
- assert len(datas["form1"]) == 3
- assert len(datas["form2"]) == 1
+ assert order == ["form1", "form2"]
- assert order["form1"] == [
+ assert datas["form1"]["order"] == [
"items/field1"
] # both field2 and field3 go to compute
- assert order["form2"] == ["items/field4"]
+ assert datas["form2"]["order"] == ["items/field4"]
- assert len(compute["form1"]) == 2
+ assert len(datas["form1"]["compute"]) == 2
assert any(
- item["variableName"] == "field2" for item in compute["form1"]
+ item["variableName"] == "field2"
+ for item in datas["form1"]["compute"]
)
assert any(
- item["variableName"] == "field3" for item in compute["form1"]
+ item["variableName"] == "field3"
+ for item in datas["form1"]["compute"]
)
@@ -46,26 +47,23 @@ def test_process_csv_missing_columns():
csv_path.write_text(csv_data)
with pytest.raises(ValueError):
- process_csv(csv_path, tmpdir, "test_protocol")
-
-
-def test_normalize_condition():
+ process_csv(csv_path)
+
+
+@pytest.mark.parametrize(
+ "condition_str,expected",
+ [
+ ("[field1] + [field2]", "field1 + field2"),
+ ("[total]*100", "total * 100"),
+ ("2+2", "2 + 2"),
+ ("3*3", "3 * 3"),
+ ("[age] = 1", "age == 1"),
+ ("[field1] = 1 or [field2] = 2", "field1 == 1 || field2 == 2"),
+ ("[age] > 18", "age > 18"),
+ ("[some_other_condition] = 1", "some_other_condition == 1"),
+ ("[weight] > 0 and [height] > 0", "weight > 0 && height > 0"),
+ ],
+)
+def test_normalize_condition(condition_str, expected):
# Test calc expressions
- assert (
- normalize_condition("[field1] + [field2]", field_type="calc")
- == "field1 + field2"
- )
- assert (
- normalize_condition("[total]*100", field_type="calc") == "total * 100"
- )
- assert normalize_condition("2+2", field_type="calc") == "2 + 2"
-
- # Test @CALCTEXT expressions
- assert normalize_condition("3*3") == "3 * 3"
-
- # Test branching logic
- assert normalize_condition("[age] = 1") == "age == 1"
- assert (
- normalize_condition("[field1] = 1 or [field2] = 2")
- == "field1 == 1 || field2 == 2"
- )
+ assert normalize_condition(condition_str) == expected
diff --git a/reproschema/tests/test_redcap2reproschema.py b/reproschema/tests/test_redcap2reproschema.py
index ff8d7b9..8c2ebe9 100644
--- a/reproschema/tests/test_redcap2reproschema.py
+++ b/reproschema/tests/test_redcap2reproschema.py
@@ -1,14 +1,12 @@
import os
import shutil
-import pytest
import yaml
from click.testing import CliRunner
from ..cli import main
-from ..redcap2reproschema import process_field_properties
-CSV_FILE_NAME = "redcap_dict.csv"
+CSV_FILE_NAME = "redcap_hbn_sample.csv"
YAML_FILE_NAME = "redcap2rs.yaml"
CSV_TEST_FILE = os.path.join(
os.path.dirname(__file__), "test_redcap2rs_data", CSV_FILE_NAME
@@ -27,10 +25,6 @@ def test_redcap2reproschema(tmpdir):
shutil.copy(CSV_TEST_FILE, str(temp_csv_file))
shutil.copy(YAML_TEST_FILE, str(temp_yaml_file))
- # Add debug output to see the content of the CSV file
- with open(str(temp_csv_file), "r") as f:
- print("CSV content:", f.read())
-
with tmpdir.as_cwd():
# Read YAML to find the expected output directory name
with open(str(temp_yaml_file), "r") as file:
@@ -52,35 +46,3 @@ def test_redcap2reproschema(tmpdir):
assert os.path.isdir(
protocol_name
), f"Expected output directory '{protocol_name}' does not exist"
-
-
-def test_process_field_properties_visibility():
- # Test case 1: No branching logic or annotations
- field_data = {"Variable / Field Name": "test_field"}
- result = process_field_properties(field_data)
- assert "isVis" not in result
-
- # Test case 2: With branching logic
- field_data = {
- "Variable / Field Name": "test_field",
- "Branching Logic (Show field only if...)": "[age] > 18",
- }
- result = process_field_properties(field_data)
- assert result["isVis"] == "age > 18"
-
- # Test case 3: With @HIDDEN annotation
- field_data = {
- "Variable / Field Name": "test_field",
- "Field Annotation": "@HIDDEN",
- }
- result = process_field_properties(field_data)
- assert result["isVis"] is False
-
- # Test case 4: With both branching logic and @HIDDEN
- field_data = {
- "Variable / Field Name": "test_field",
- "Branching Logic (Show field only if...)": "[age] > 18",
- "Field Annotation": "@HIDDEN",
- }
- result = process_field_properties(field_data)
- assert result["isVis"] is False
diff --git a/reproschema/tests/test_redcap2rs_data/redcap_dict.csv b/reproschema/tests/test_redcap2rs_data/redcap_dict.csv
deleted file mode 100644
index 6f48394..0000000
--- a/reproschema/tests/test_redcap2rs_data/redcap_dict.csv
+++ /dev/null
@@ -1,31 +0,0 @@
-"Variable / Field Name","Form Name","Section Header","Field Type","Field Label","Choices, Calculations, OR Slider Labels","Field Note","Text Validation Type OR Show Slider Number","Text Validation Min","Text Validation Max",Identifier?,"Branching Logic (Show field only if...)","Required Field?","Custom Alignment","Question Number (surveys only)","Matrix Group Name","Matrix Ranking?","Field Annotation"
-record_id,autism_parenting_stress_index_apsi,,text,"Record ID",,,,,,,,,,,,,
-apsi_date,autism_parenting_stress_index_apsi,"Autism Parenting Stress Index for the Qigong Sensory Training Program Instructions: 1. Before beginning Qigong Sensory Training therapy with your child, complete the form on the following page. 2. Enter the date, name of your child, and who is completing the checklist. (It is very important that the same parent/caretaker complete the form each time the form is used.) 3. Choose the response for each item that most accurately describes your child. 4. Add all of the numbers chosen. 5. Enter total into the space provided. After using Qigong Sensory Training therapy on your child once a day for a five months, have the same parent complete the form again. Total numbers circled. Compare this number to the number at the beginning. If Qigong Sensory Training therapy is being implemented successfully, the total number should decrease over time.",text,Date:,,,date_ymd,,,,,,,,,,
-apsi_name_of_child,autism_parenting_stress_index_apsi,,text,"Name of child:",,,,,,,,,,,,,
-apsi_person_completing,autism_parenting_stress_index_apsi,,text,"Person completing checklist:",,,,,,,,,,,,,
-apsi_social_dev,autism_parenting_stress_index_apsi,"Stress Ratings Please rate the following aspects of your child's health according to how much stress it causes you and/or your family by clicking on the button that best describes your situation.",radio,"Your child's social development ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_communicate,autism_parenting_stress_index_apsi,,radio,"Your child's ability to communicate ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_tantrums,autism_parenting_stress_index_apsi,,radio,"Tantrums/meltdowns ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_agressive,autism_parenting_stress_index_apsi,,radio,"Aggressive behavior (siblings, peers) ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_self_injure,autism_parenting_stress_index_apsi,,radio,"Self-injurious behavior ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_transitions,autism_parenting_stress_index_apsi,,radio,"Difficulty making transitions from one activity to another ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_sleep,autism_parenting_stress_index_apsi,,radio,"Sleep problems ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_diet,autism_parenting_stress_index_apsi,,radio,"Your child's diet ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_bowel,autism_parenting_stress_index_apsi,,radio,"Bowel problems (diarrhea, constipation) ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_potty,autism_parenting_stress_index_apsi,,radio,"Potty training ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_not_close,autism_parenting_stress_index_apsi,,radio,"Not feeling close to your child ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_accepted,autism_parenting_stress_index_apsi,,radio,"Concern for the future of your child being accepted by others ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_independently,autism_parenting_stress_index_apsi,,radio,"Concern for the future of your child living independently ","0, 0 - Not stressful | 1, 1 - Sometimes creates stress | 2, 2 - Often creates stress | 3, 3 - Very stressful on a daily basis | 5, 5 - So stressful sometimes we feel we can't cope",,,,,,,,,,,,
-apsi_total,autism_parenting_stress_index_apsi,,text,Total,,,integer,,,,,,,,,,
-cams_r_1,cognitive_and_affective_mindfulness_scalerevised_c,"Instructions: People have a variety of ways of relating to their thoughts and feelings. For each of the items below, rate how much each of these ways applies to you.",radio,"1. It is easy for me to concentrate on what I am doing.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_2,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"2. I am preoccupied by the future.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_3,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"3. I can tolerate emotional pain.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_4,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"4. I can accept things I cannot change.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_5,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"5. I can usually describe how I feel at the moment in considerable detail.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_6,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"6. I am easily distracted.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_7,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"7. I am preoccupied by the past.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_8,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"8. It's easy for me to keep track of my thoughts and feelings.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_9,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"9. I try to notice my thoughts without judging them.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_10,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"10. I am able to accept the thoughts and feelings I have.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_11,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"11. I am able to focus on the present moment.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
-cams_r_12,cognitive_and_affective_mindfulness_scalerevised_c,,radio,"12. I am able to pay close attention to one thing for a long period of time.","1, 1 - Rarely/Not at all | 2, 2 - Sometimes | 3, 3 - Often | 4, 4 - Almost Always",,,,,,,,,,,,
diff --git a/reproschema/tests/test_redcap2rs_data/redcap_hbn_sample.csv b/reproschema/tests/test_redcap2rs_data/redcap_hbn_sample.csv
new file mode 100644
index 0000000..d0e2e98
--- /dev/null
+++ b/reproschema/tests/test_redcap2rs_data/redcap_hbn_sample.csv
@@ -0,0 +1,522 @@
+"Variable / Field Name","Form Name","Section Header","Field Type","Field Label","Choices, Calculations, OR Slider Labels","Field Note","Text Validation Type OR Show Slider Number","Text Validation Min","Text Validation Max",Identifier?,"Branching Logic (Show field only if...)","Required Field?","Custom Alignment","Question Number (surveys only)","Matrix Group Name","Matrix Ranking?","Field Annotation"
+record_id,setup,,text,"Record ID",,,,,,,,y,,,,,
+setup_lmp,setup,,text,"Last menstrual period (LMP)",,,date_mdy,,,,,y,,,,,
+setup_edd,setup,,text,"Estimated date of delivery (EDD)",,,date_ymd,,,,,y,,,,,
+setup_delivery,setup,,text,"Actual date of delivery",,,date_ymd,,,,,y,,,,,
+setup_offset,setup,,text,"Offset (in weeks) between anonymized birthdate and EDD",,,number,,,,,y,,,,,
+recruitment_period,setup,,radio,"Timepoint of participant recruitment","1, Prenatal | 2, Postnatal",,,,,,,y,,,,,
+setup_sex,setup,,radio,"Sex assigned at birth","M, Male | F, Female | O, Other",,,,,,,,,,,,
+admin_caregiver_001,setup_l,,yesno,"Has the caregiver changed since the last study visit?",,,,,,,,y,,,,,
+admin_caregiver_002,setup_l,,radio,"Caregiver type for this visit","1, CG Type A (Temporary alternative caregiver) | 2, CG Type B (Change in primary caregiver (placement only) without change in legal custody (but BP unable to complete visit)) | 3, CG Type C (Change in joint custody) | 4, CG Type D (Child removed from BP and placed in foster care (change in placement)) | 5, CG Type E (Change in legal custody and placement, e.g. adoption) | 6, CG Type F (Birth mother)",,,,,,,y,,,,,
+setup_onsite_started,setup_l,,yesno,"Onsite visit started?",,,,,,,,y,,,,,
+setup_event_start,setup_l,,text,"Visit window start date",,,date_ymd,,,,,y,,,,,
+setup_event_end,setup_l,,text,"Visit window end date",,,date_ymd,,,,,y,,,,,
+url_vineland,setup_l,,text,"Vineland URL",,,,,,,,,,,,,
+visit_start_instr01,visit_start,,descriptive,"If you have started the on-site visit for this participant, click 'Submit'",,,,,,,,,,,,,
+remote_introduction,remote_survey_introduction,,descriptive,"Thank you for participating in the Healthy Brain and Child Development (HBCD) Study! These surveys will help us learn more about your child's development. There will be questions about your child, yourself, and your family and home.
+
+You can only answer each question once, but you can change your answers before you submit each survey. There are no right or wrong answers, but it's important to answer truthfully. Some questions are about things from the past or what you've seen. If you can't remember or are not sure, just make your best guess. Your answers will be kept confidential.
+
+When you need breaks, you can take one between surveys. Just be sure to finish and submit the survey you're doing before your leave the page so your answers are saved. When you click the survey link again, you will start the next survey.
+
+If you have any questions or concerns, we are happy to help! Please contact your HBCD team for more information.
+
+Thank you for your participation!",,,,,,,,,,,,,
+child_introduction_v4,child_survey_introduction,,descriptive,"This first set of surveys will ask you all about your child, how they are growing, and the new things they are learning. There are no right or wrong answers. We want to learn about your child from you! Some surveys will be short and others will be longer. You can take breaks as needed. There are 11 surveys in this section and all together they will take a little over an hour to complete.
This first set of surveys will ask you all about your child, how they are growing, and the new things they are learning. There are no right or wrong answers. We want to learn about your child from you! Some surveys will be short and others will be longer. You can take breaks as needed. There are 13 surveys in this section and all together they will take about an hour to complete.
This first set of surveys will ask you all about your child, how they are growing, and the new things they are learning. There are no right or wrong answers. We want to learn about your child from you! Some surveys will be short and others will be longer. You can take breaks as needed. There are 9 surveys in this section and all together they will take about an hour to complete.
Thank you for completing questions about your child! That was the longest section of the surveys. Next we'd like to ask some questions about you. These questions will ask about your health, your thoughts and feelings, support and stress, and your use of medications and substances. As a reminder, your responses are confidential. There are 4 surveys in this section and all together they will take about 20-30 minutes.
Thank you for completing questions about your child! That was the longest section of the surveys. Next we'd like to ask some questions about you. These questions will ask about your health, your thoughts and feelings, support and stress, and your use of medications and substances. As a reminder, your responses are confidential. There are 8 surveys in this section and all together they will take about 20-30 minutes.
Thank you for completing questions about your child! That was the longest section of the surveys. Next we'd like to ask some questions about you. These questions will ask about your health, your thoughts and feelings, support and stress, and your use of medications and substances. As a reminder, your responses are confidential. There are 5 surveys in this section and all together they will take about 20-30 minutes.
Thank you for completing those surveys! This final set of surveys is the shortest and will ask about your family and your home. These questions will give us a bigger picture of your child's day-to-day life and can help us understand their development. There are just 3 surveys and all together they will take about 10 minutes.
| How tall are you without shoes? | Â {pex_bm_health_preg_i_healthhx_007_i_01} ft {pex_bm_health_preg_i_healthhx_007_i_02} in {pex_bm_health_preg_i_healthhx_007_i_dk} |
",,,,,,,,,,,,,
+pex_bm_health_preg_i_healthhx_007_i_dk,pex_bm_health_preg_i_healthhx,,radio,"Height don't know / decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_007_i_01] = '' AND [pex_bm_health_preg_i_healthhx_007_i_02] =''",y,,,,,
+pex_bm_health_preg_i_healthhx_008,pex_bm_health_preg_i_healthhx,,calc,"Pre-pregnancy height, centimeters","([pex_bm_health_preg_i_healthhx_007_i_01] * 12 + [pex_bm_health_preg_i_healthhx_007_i_02]) * 2.54",,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_009_i_00,pex_bm_health_preg_i_healthhx,,descriptive," | Just before you got pregnant, how much did you weigh in pounds? | Â {pex_bm_health_preg_i_healthhx_009} {pex_bm_health_preg_i_healthhx_009_i_dk} |
",,,,,,,,,,,,,
+pex_bm_health_preg_i_healthhx_009,pex_bm_health_preg_i_healthhx,,dropdown,"Just before you got pregnant, how much did you weigh in pounds?","90, 90 | 91, 91 | 92, 92 | 93, 93 | 94, 94 | 95, 95 | 96, 96 | 97, 97 | 98, 98 | 99, 99 | 100, 100 | 101, 101 | 102, 102 | 103, 103 | 104, 104 | 105, 105 | 106, 106 | 107, 107 | 108, 108 | 109, 109 | 110, 110 | 111, 111 | 112, 112 | 113, 113 | 114, 114 | 115, 115 | 116, 116 | 117, 117 | 118, 118 | 119, 119 | 120, 120 | 121, 121 | 122, 122 | 123, 123 | 124, 124 | 125, 125 | 126, 126 | 127, 127 | 128, 128 | 129, 129 | 130, 130 | 131, 131 | 132, 132 | 133, 133 | 134, 134 | 135, 135 | 136, 136 | 137, 137 | 138, 138 | 139, 139 | 140, 140 | 141, 141 | 142, 142 | 143, 143 | 144, 144 | 145, 145 | 146, 146 | 147, 147 | 148, 148 | 149, 149 | 150, 150 | 151, 151 | 152, 152 | 153, 153 | 154, 154 | 155, 155 | 156, 156 | 157, 157 | 158, 158 | 159, 159 | 160, 160 | 161, 161 | 162, 162 | 163, 163 | 164, 164 | 165, 165 | 166, 166 | 167, 167 | 168, 168 | 169, 169 | 170, 170 | 171, 171 | 172, 172 | 173, 173 | 174, 174 | 175, 175 | 176, 176 | 177, 177 | 178, 178 | 179, 179 | 180, 180 | 181, 181 | 182, 182 | 183, 183 | 184, 184 | 185, 185 | 186, 186 | 187, 187 | 188, 188 | 189, 189 | 190, 190 | 191, 191 | 192, 192 | 193, 193 | 194, 194 | 195, 195 | 196, 196 | 197, 197 | 198, 198 | 199, 199 | 200, 200 | 201, 201 | 202, 202 | 203, 203 | 204, 204 | 205, 205 | 206, 206 | 207, 207 | 208, 208 | 209, 209 | 210, 210 | 211, 211 | 212, 212 | 213, 213 | 214, 214 | 215, 215 | 216, 216 | 217, 217 | 218, 218 | 219, 219 | 220, 220 | 221, 221 | 222, 222 | 223, 223 | 224, 224 | 225, 225 | 226, 226 | 227, 227 | 228, 228 | 229, 229 | 230, 230 | 231, 231 | 232, 232 | 233, 233 | 234, 234 | 235, 235 | 236, 236 | 237, 237 | 238, 238 | 239, 239 | 240, 240 | 241, 241 | 242, 242 | 243, 243 | 244, 244 | 245, 245 | 246, 246 | 247, 247 | 248, 248 | 249, 249 | 250, 250 | 251, 251 | 252, 252 | 253, 253 | 254, 254 | 255, 255 | 256, 256 | 257, 257 | 258, 258 | 259, 259 | 260, 260 | 261, 261 | 262, 262 | 263, 263 | 264, 264 | 265, 265 | 266, 266 | 267, 267 | 268, 268 | 269, 269 | 270, 270 | 271, 271 | 272, 272 | 273, 273 | 274, 274 | 275, 275 | 276, 276 | 277, 277 | 278, 278 | 279, 279 | 280, 280 | 281, 281 | 282, 282 | 283, 283 | 284, 284 | 285, 285 | 286, 286 | 287, 287 | 288, 288 | 289, 289 | 290, 290 | 291, 291 | 292, 292 | 293, 293 | 294, 294 | 295, 295 | 296, 296 | 297, 297 | 298, 298 | 299, 299 | 300, 300 | 301, 301 | 302, 302 | 303, 303 | 304, 304 | 305, 305 | 306, 306 | 307, 307 | 308, 308 | 309, 309 | 310, 310 | 311, 311 | 312, 312 | 313, 313 | 314, 314 | 315, 315 | 316, 316 | 317, 317 | 318, 318 | 319, 319 | 320, 320 | 321, 321 | 322, 322 | 323, 323 | 324, 324 | 325, 325 | 326, 326 | 327, 327 | 328, 328 | 329, 329 | 330, 330 | 331, 331 | 332, 332 | 333, 333 | 334, 334 | 335, 335 | 336, 336 | 337, 337 | 338, 338 | 339, 339 | 340, 340 | 341, 341 | 342, 342 | 343, 343 | 344, 344 | 345, 345 | 346, 346 | 347, 347 | 348, 348 | 349, 349 | 350, 350 | 351, 351 | 352, 352 | 353, 353 | 354, 354 | 355, 355 | 356, 356 | 357, 357 | 358, 358 | 359, 359 | 360, 360 | 361, 361 | 362, 362 | 363, 363 | 364, 364 | 365, 365 | 366, 366 | 367, 367 | 368, 368 | 369, 369 | 370, 370 | 371, 371 | 372, 372 | 373, 373 | 374, 374 | 375, 375 | 376, 376 | 377, 377 | 378, 378 | 379, 379 | 380, 380 | 381, 381 | 382, 382 | 383, 383 | 384, 384 | 385, 385 | 386, 386 | 387, 387 | 388, 388 | 389, 389 | 390, 390 | 391, 391 | 392, 392 | 393, 393 | 394, 394 | 395, 395 | 396, 396 | 397, 397 | 398, 398 | 399, 399 | 400, 400",,autocomplete,,,,"[pex_bm_health_preg_i_healthhx_009_i_dk] = '' ",y,,,,,
+pex_bm_health_preg_i_healthhx_009_i_dk,pex_bm_health_preg_i_healthhx,,radio,"Weight don't know / decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_009] = '' ",y,,,,,
+pex_bm_health_preg_i_healthhx_010,pex_bm_health_preg_i_healthhx,,calc,"Pre-Pregnancy weight, kilograms",([pex_bm_health_preg_i_healthhx_009]/2.2046),,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_011,pex_bm_health_preg_i_healthhx,,calc,"Pre-Pregnancy BMI","[pex_bm_health_preg_i_healthhx_010] * 10000 / ([pex_bm_health_preg_i_healthhx_008] * [pex_bm_health_preg_i_healthhx_008])",,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_001_i_00_i_pre,pex_bm_health_preg_i_healthhx,"Pregnancy History",descriptive," | Including live births, stillbirths, miscarriages, abortions, and tubal and other ectopic pregnancies, how many times have you been pregnant? (Be sure to count your current pregnancy) | Â {pex_bm_health_preg_i_healthhx_i_preghx_001} {pex_bm_health_preg_i_healthhx_i_preghx_001_i_dk} |
",,,,,,,"[screening_arm_1][recruitment_period] ='1'",,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_001,pex_bm_health_preg_i_healthhx,,dropdown,"number of pregancies pre enrollment","1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | 6, 6 | 7, 7 | 8, 8 | 9, 9 | 10, 10 | 11, 11 | 12, 12 | 13, 13 | 14, 14 | 15, 15",,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_001_i_dk,pex_bm_health_preg_i_healthhx,,radio,"# of pregnancies pre enrollment dk","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_001_i_00_i_post,pex_bm_health_preg_i_healthhx,,descriptive," | Including live births, stillbirths, miscarriages, abortions, and tubal and other ectopic pregnancies, how many times have you been pregnant? (Be sure to count your recent pregnancy) | Â {pex_bm_health_preg_i_healthhx_i_preghx_001_post} {pex_bm_health_preg_i_healthhx_i_preghx_001_i_dk_post} |
",,,,,,,"[screening_arm_1][recruitment_period] = '2'",,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_001_post,pex_bm_health_preg_i_healthhx,,dropdown,"# of pregnancy post enrollment ","1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | 6, 6 | 7, 7 | 8, 8 | 9, 9 | 10, 10 | 11, 11 | 12, 12 | 13, 13 | 14, 14 | 15, 15",,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001_i_dk_post] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_001_i_dk_post,pex_bm_health_preg_i_healthhx,,radio,"# of pregnancies post enrollment dk","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001_post] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_002_i_00,pex_bm_health_preg_i_healthhx,,descriptive," | How many times has your pregnancy ended in a live birth? | Â {pex_bm_health_preg_i_healthhx_i_preghx_002} {pex_bm_health_preg_i_healthhx_i_preghx_002_i_dk} |
",,,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001] >1",,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_002,pex_bm_health_preg_i_healthhx,,text,"How many times has your pregnancy ended in a live birth?",,,number,0,[pex_bm_health_preg_i_healthhx_i_preghx_001],,"[pex_bm_health_preg_i_healthhx_i_preghx_001] >1 AND [pex_bm_health_preg_i_healthhx_i_preghx_002_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_002_i_dk,pex_bm_health_preg_i_healthhx,,radio,"live birth dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001] >1 AND [pex_bm_health_preg_i_healthhx_i_preghx_002] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_003_i_pre,pex_bm_health_preg_i_healthhx,,text,"On what date did your last pregnancy end (regardless of the outcome)?",,,date_mdy,,[screening_arm_1][setup_lmp],,"[pex_bm_health_preg_i_healthhx_i_preghx_001] >1 AND [screening_arm_1][recruitment_period] ='1'",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_003_i_post,pex_bm_health_preg_i_healthhx,,text,"On what date did your last pregnancy prior to this most recent one end (regardless of the outcome)?",,,date_mdy,,[screening_arm_1][setup_lmp],,"[pex_bm_health_preg_i_healthhx_i_preghx_001] >1 AND [recruitment_period] = '2'",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_004_i_pre,pex_bm_health_preg_i_healthhx,,radio,"Have you ever given birth via Cesarean delivery?","0, No | 1, Yes | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001] >1 AND [screening_arm_1][recruitment_period] ='1'",y,,,,,
+pex_bm_health_preg_i_healthhx_i_preghx_004_i_post,pex_bm_health_preg_i_healthhx,,radio,"Before this delivery, have you ever given birth via Cesarean delivery?","0, No | 1, Yes | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_preghx_001] >1 AND [recruitment_period] = '2'",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_001,pex_bm_health_preg_i_healthhx,"Current Pregnancy - ART",radio,"To become pregnant with this pregnancy, did you seek any assisted reproductive technologies (like fertility drugs and/or handling of egg, sperm, or embryos)? ","0, No | 1, Yes | 999, Don't know | 777, Decline to answer",,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_002,pex_bm_health_preg_i_healthhx,,checkbox,"Why did you seek assisted reproductive technology (check all that apply)?","1, Infertility | 2, Same sex relationship | 3, Genetic concerns | 4, Sex selection or family balancing | 5, Previously preserved embryos prior to chemotherapy or other medical interventions | 6, Other | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_001] = '1'",y,,,,," @NONEOFTHEABOVE='777,999'"
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003,pex_bm_health_preg_i_healthhx,,checkbox,"What treatments did you receive (check all that apply):","1, Artificial insemination | 2, In-vitro fertilization | 3, Fertility-enhancing medications | 4, ICSI | 5, Pre-implantation genetic screening | 6, Donor egg | 7, Donor sperm | 8, Donor embryo | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_001] = '1'",y,,,,," @NONEOFTHEABOVE='777,999'"
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_004_i_00,pex_bm_health_preg_i_healthhx,,descriptive,"Age of egg donor {pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_004} {pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_004_dk}",,,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(6)] = '1' OR [pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(8)] = '1'",,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_004,pex_bm_health_preg_i_healthhx,,dropdown,"Age of egg donor","18, 18 | 19, 19 | 20, 20 | 21, 21 | 22, 22 | 23, 23 | 24, 24 | 25, 25 | 26, 26 | 27, 27 | 28, 28 | 29, 29 | 30, 30 | 31, 31 | 32, 32 | 33, 33 | 34, 34 | 35, 35 | 36, 36 | 37, 37 | 38, 38 | 39, 39 | 40, 40",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_004_dk] =''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_004_dk,pex_bm_health_preg_i_healthhx,,radio,"Age of egg donor don't know/decline to answer","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_004] =''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_005,pex_bm_health_preg_i_healthhx,,checkbox,"Ethnicity of egg donor","0, American Indian or Alaska Native (For example: Aztec, Blackfeet Tribe, Mayan, Navajo Nation, Native Village of Barrow (Utqiagvik) Inupiat Traditional Government, Nome Eskimo Community, etc.) | 1, Asian (For example: Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.) | 2, Black, African American, or African (For example: African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.) | 3, Hispanic, Latino, or Spanish (For example: Colombian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.) | 4, Middle Eastern or North African (For example: Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.) | 5, Native Hawaiian or other Pacific Islander (For example: Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.) | 6, White (For example: English, European, French, German, Irish, Italian, Polish, etc.) | 7, None of these fully describe me / Other |999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(6)] = '1' OR [pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(8)] = '1'",y,,,,," @NONEOFTHEABOVE='777,999'"
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_006_i_00,pex_bm_health_preg_i_healthhx,,descriptive,"Age of sperm donor {pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_006} {pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_006_dk}",,,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(7)] = '1' OR [pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(8)] = '1'",,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_006,pex_bm_health_preg_i_healthhx,,dropdown,"Age of sperm donor","18, 18 | 19, 19 | 20, 20 | 21, 21 | 22, 22 | 23, 23 | 24, 24 | 25, 25 | 26, 26 | 27, 27 | 28, 28 | 29, 29 | 30, 30 | 31, 31 | 32, 32 | 33, 33 | 34, 34 | 35, 35 | 36, 36 | 37, 37 | 38, 38 | 39, 39 | 40, 40",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_006_dk] =''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_006_dk,pex_bm_health_preg_i_healthhx,,radio,"Age of sperm donor don't know/decline to answer","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_006] =''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_007,pex_bm_health_preg_i_healthhx,,checkbox,"Ethnicity of sperm donor","0, American Indian or Alaska Native (For example: Aztec, Blackfeet Tribe, Mayan, Navajo Nation, Native Village of Barrow (Utqiagvik) Inupiat Traditional Government, Nome Eskimo Community, etc.) | 1, Asian (For example: Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.) | 2, Black, African American, or African (For example: African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.) | 3, Hispanic, Latino, or Spanish (For example: Colombian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.) | 4, Middle Eastern or North African (For example: Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.) | 5, Native Hawaiian or other Pacific Islander (For example: Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.) | 6, White (For example: English, European, French, German, Irish, Italian, Polish, etc.) | 7, None of these fully describe me / Other |999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(7)] = '1' OR [pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_003(8)] = '1'",y,,,,," @NONEOFTHEABOVE='777,999'"
+pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_008,pex_bm_health_preg_i_healthhx,,radio,"Was this pregnancy the result of this treatment?","0, No | 1, Yes | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_i_art_001] = '1'",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_001,pex_bm_health_preg_i_healthhx,"Current Pregnancy ",radio,"Thinking back to just before you got pregnant, how did you feel about becoming pregnant?","1, I wanted to be pregnant sooner | 2, I wanted to be pregnant then | 3, I wanted to be pregnant later | 4, I didn't want to be pregnant then or ever | 5, I wasn't sure what I wanted | 999, Don't know | 777, Decline to answer",,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_002,pex_bm_health_preg_i_healthhx,,radio,"Which of the following statements best describes you during the three months before you got pregnant?","1, I was trying to get pregnant | 2, I was not trying to get pregnant but I also was not trying to keep from getting pregnant | 3, I was trying to keep from getting pregnant | 999, Don't know | 777, Decline to answer",,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_00,pex_bm_health_preg_i_healthhx,,descriptive," | How many weeks or months pregnant were you when you had your first visit for prenatal care? Select number and unit (week or months; weeks preferred). | Â {pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_01} {pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_02} {pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_dk} |
",,,,,,,,,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_01,pex_bm_health_preg_i_healthhx,,dropdown," First visit for prenatal care (weeks or months)","1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | 6, 6 | 7, 7 | 8, 8 | 9, 9 | 10, 10 | 11, 11 | 12, 12 | 13, 13 | 14, 14 | 15, 15 | 16, 16 | 17, 17 | 18, 18 | 19, 19 | 20, 20 | 21, 21 | 22, 22 | 23, 23 | 24, 24 | 25, 25 | 26, 26 | 27, 27 | 28, 28 | 29, 29 | 30, 30 | 31, 31 | 32, 32 | 33, 33 | 34, 34 | 35, 35 | 36, 36 | 37, 37 | 38, 38 | 39, 39 | 40, 40 | 41, 41 | 42, 42",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_02,pex_bm_health_preg_i_healthhx,,radio," First visit for prenatal care (unit)","1, weeks | 2, months",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_dk,pex_bm_health_preg_i_healthhx,,radio," First visit for prenatal care dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_01] ='' AND [pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_02] =''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_004,pex_bm_health_preg_i_healthhx,,calc,"Calculated Gestational Age at initiation of prenatal care","if( [pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_02] = 1, [pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_01], if([pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_02] = 2, [pex_bm_health_preg_i_healthhx_i_pregcurr_003_i_01] * 4, """" ))",,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_005_i_00,pex_bm_health_preg_i_healthhx,,descriptive,"What is your current weight in pounds? {pex_bm_health_preg_i_healthhx_i_pregcurr_005} {pex_bm_health_preg_i_healthhx_i_pregcurr_005_i_dk}",,,,,,,,,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_005,pex_bm_health_preg_i_healthhx,,dropdown,"What is your current weight in pounds? ","90, 90 | 91, 91 | 92, 92 | 93, 93 | 94, 94 | 95, 95 | 96, 96 | 97, 97 | 98, 98 | 99, 99 | 100, 100 | 101, 101 | 102, 102 | 103, 103 | 104, 104 | 105, 105 | 106, 106 | 107, 107 | 108, 108 | 109, 109 | 110, 110 | 111, 111 | 112, 112 | 113, 113 | 114, 114 | 115, 115 | 116, 116 | 117, 117 | 118, 118 | 119, 119 | 120, 120 | 121, 121 | 122, 122 | 123, 123 | 124, 124 | 125, 125 | 126, 126 | 127, 127 | 128, 128 | 129, 129 | 130, 130 | 131, 131 | 132, 132 | 133, 133 | 134, 134 | 135, 135 | 136, 136 | 137, 137 | 138, 138 | 139, 139 | 140, 140 | 141, 141 | 142, 142 | 143, 143 | 144, 144 | 145, 145 | 146, 146 | 147, 147 | 148, 148 | 149, 149 | 150, 150 | 151, 151 | 152, 152 | 153, 153 | 154, 154 | 155, 155 | 156, 156 | 157, 157 | 158, 158 | 159, 159 | 160, 160 | 161, 161 | 162, 162 | 163, 163 | 164, 164 | 165, 165 | 166, 166 | 167, 167 | 168, 168 | 169, 169 | 170, 170 | 171, 171 | 172, 172 | 173, 173 | 174, 174 | 175, 175 | 176, 176 | 177, 177 | 178, 178 | 179, 179 | 180, 180 | 181, 181 | 182, 182 | 183, 183 | 184, 184 | 185, 185 | 186, 186 | 187, 187 | 188, 188 | 189, 189 | 190, 190 | 191, 191 | 192, 192 | 193, 193 | 194, 194 | 195, 195 | 196, 196 | 197, 197 | 198, 198 | 199, 199 | 200, 200 | 201, 201 | 202, 202 | 203, 203 | 204, 204 | 205, 205 | 206, 206 | 207, 207 | 208, 208 | 209, 209 | 210, 210 | 211, 211 | 212, 212 | 213, 213 | 214, 214 | 215, 215 | 216, 216 | 217, 217 | 218, 218 | 219, 219 | 220, 220 | 221, 221 | 222, 222 | 223, 223 | 224, 224 | 225, 225 | 226, 226 | 227, 227 | 228, 228 | 229, 229 | 230, 230 | 231, 231 | 232, 232 | 233, 233 | 234, 234 | 235, 235 | 236, 236 | 237, 237 | 238, 238 | 239, 239 | 240, 240 | 241, 241 | 242, 242 | 243, 243 | 244, 244 | 245, 245 | 246, 246 | 247, 247 | 248, 248 | 249, 249 | 250, 250 | 251, 251 | 252, 252 | 253, 253 | 254, 254 | 255, 255 | 256, 256 | 257, 257 | 258, 258 | 259, 259 | 260, 260 | 261, 261 | 262, 262 | 263, 263 | 264, 264 | 265, 265 | 266, 266 | 267, 267 | 268, 268 | 269, 269 | 270, 270 | 271, 271 | 272, 272 | 273, 273 | 274, 274 | 275, 275 | 276, 276 | 277, 277 | 278, 278 | 279, 279 | 280, 280 | 281, 281 | 282, 282 | 283, 283 | 284, 284 | 285, 285 | 286, 286 | 287, 287 | 288, 288 | 289, 289 | 290, 290 | 291, 291 | 292, 292 | 293, 293 | 294, 294 | 295, 295 | 296, 296 | 297, 297 | 298, 298 | 299, 299 | 300, 300 | 301, 301 | 302, 302 | 303, 303 | 304, 304 | 305, 305 | 306, 306 | 307, 307 | 308, 308 | 309, 309 | 310, 310 | 311, 311 | 312, 312 | 313, 313 | 314, 314 | 315, 315 | 316, 316 | 317, 317 | 318, 318 | 319, 319 | 320, 320 | 321, 321 | 322, 322 | 323, 323 | 324, 324 | 325, 325 | 326, 326 | 327, 327 | 328, 328 | 329, 329 | 330, 330 | 331, 331 | 332, 332 | 333, 333 | 334, 334 | 335, 335 | 336, 336 | 337, 337 | 338, 338 | 339, 339 | 340, 340 | 341, 341 | 342, 342 | 343, 343 | 344, 344 | 345, 345 | 346, 346 | 347, 347 | 348, 348 | 349, 349 | 350, 350 | 351, 351 | 352, 352 | 353, 353 | 354, 354 | 355, 355 | 356, 356 | 357, 357 | 358, 358 | 359, 359 | 360, 360 | 361, 361 | 362, 362 | 363, 363 | 364, 364 | 365, 365 | 366, 366 | 367, 367 | 368, 368 | 369, 369 | 370, 370 | 371, 371 | 372, 372 | 373, 373 | 374, 374 | 375, 375 | 376, 376 | 377, 377 | 378, 378 | 379, 379 | 380, 380 | 381, 381 | 382, 382 | 383, 383 | 384, 384 | 385, 385 | 386, 386 | 387, 387 | 388, 388 | 389, 389 | 390, 390 | 391, 391 | 392, 392 | 393, 393 | 394, 394 | 395, 395 | 396, 396 | 397, 397 | 398, 398 | 399, 399 | 400, 400",,autocomplete,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_005_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_005_i_dk,pex_bm_health_preg_i_healthhx,,radio,"Current weight dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_pregcurr_005] = ''",y,,,,,
+pex_bm_health_preg_i_healthhx_i_pregcurr_006,pex_bm_health_preg_i_healthhx,,calc,"Current weight in kg",([pex_bm_health_preg_i_healthhx_i_pregcurr_005]/2.2046),,,,,,,y,,,,,
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_001,pex_bm_health_preg_i_healthhx,"Pregnancy Exposures
+
+Prenatal Vitamins, Multivitamins, Folic Acid and Herbal Supplements",text,"Trimester 1 (start)",,,date_mdy,,,,,y,,,,," @CALCDATE([screening_arm_1][setup_lmp], 0, ""d"") @HIDDEN"
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_002,pex_bm_health_preg_i_healthhx,,text,"Trimester 1 (end)",,,date_mdy,,,,,y,,,,," @CALCDATE([screening_arm_1][setup_lmp], 84, ""d"") @HIDDEN"
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_003,pex_bm_health_preg_i_healthhx,,text,"Trimester 2 (start)",,,date_mdy,,,,,y,,,,," @CALCDATE([screening_arm_1][setup_lmp], 85, ""d"") @HIDDEN"
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_004,pex_bm_health_preg_i_healthhx,,text,"Trimester 2 (end)",,,date_mdy,,,,,y,,,,," @CALCDATE([screening_arm_1][setup_lmp], 168, ""d"") @HIDDEN"
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_005,pex_bm_health_preg_i_healthhx,,text,"Trimester 3 (start)",,,date_mdy,,,,,y,,,,," @CALCDATE([screening_arm_1][setup_lmp], 169, ""d"") @HIDDEN"
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_006,pex_bm_health_preg_i_healthhx,,radio,"Were you taking prenatal vitamins or a folic acid containing vitamin when you had your last menstrual period ([screening_arm_1][setup_lmp]) or since?","0, No | 1, Yes | 999, Don't know | 777, Decline to answer",,,,,,,y,RH,,,,
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_006_i_01,pex_bm_health_preg_i_healthhx,,text,"What day did you start taking these vitamins? (If you starting taking them prior to your last menstrual period ([screening_arm_1][setup_lmp]), please enter the date of your last menstrual period.)",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_healthhx_i_exp_i_pnv_006] = '1'",y,RH,,,,
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_006_i_02,pex_bm_health_preg_i_healthhx,,radio,"Have you stopped taking these vitamins? ","0, No, continuing to use | 1, Yes | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_healthhx_i_exp_i_pnv_006] = ""1""",y,,,,,
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_006_i_03,pex_bm_health_preg_i_healthhx,,text,"What day did you stop taking these vitamins?",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_healthhx_i_exp_i_pnv_006_i_02] = ""1""",y,,,,,
+pex_bm_health_preg_i_healthhx_i_exp_i_pnv_011,pex_bm_health_preg_i_healthhx,,checkbox,"Since your last menstrual period, have you had indoor exposure to second-hand smoke from any of the following substances? Check all that apply","1, Cigarettes | 2, Marijuana | 3, Methamphetamine | 4, None | 999, Don't know | 777, Decline to answer",,,,,,,y,,,,," @NONEOFTHEABOVE='777,999'"
+pex_bm_health_preg_i_illness_lang,pex_bm_health_preg_i_illness,"Illnesses During Pregnancy",radio,Language,"en, English | es, Spanish",,,,,,,y,,,,," @HIDDEN @LANGUAGE-CURRENT-SURVEY"
+pex_bm_health_preg_i_illness_i_covid_001,pex_bm_health_preg_i_illness,,radio,"Since your last menstrual period on [screening_arm_1][setup_lmp], have you tested positive for SARS-CoV-2, the virus that causes COVID-19?
+
+","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,,,y,,,,,
+pex_bm_health_preg_i_illness_i_covid_002_i_00,pex_bm_health_preg_i_illness,,descriptive,"Since your last menstrual period on [screening_arm_1][setup_lmp], how many times have you tested positive for SARS-CoV-2, the virus that causes COVID-19? {pex_bm_health_preg_i_illness_i_covid_002} {pex_bm_health_preg_i_illness_i_covid_002_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_i_covid_001] = '1'",,,,,,
+pex_bm_health_preg_i_illness_i_covid_002,pex_bm_health_preg_i_illness,,dropdown,"Since your last menstrual period on [screening_arm_1][setup_lmp], how many times have you tested positive for SARS-CoV-2, the virus that causes COVID-19?","1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5",,,,,," [pex_bm_health_preg_i_illness_i_covid_002_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_002_i_dk,pex_bm_health_preg_i_illness,,radio,"number covid dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_003_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the date of your first positive test? {pex_bm_health_preg_i_illness_i_covid_003_i_01} {pex_bm_health_preg_i_illness_i_covid_003_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 1",,,,,,
+pex_bm_health_preg_i_illness_i_covid_003_i_01,pex_bm_health_preg_i_illness,,text,"What was the date of your first positive test?",,,date_mdy,,today,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 1 AND [pex_bm_health_preg_i_illness_i_covid_003_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_003_i_dk,pex_bm_health_preg_i_illness,,radio,"first date covid dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 1 AND [pex_bm_health_preg_i_illness_i_covid_003_i_01] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_003_i_02,pex_bm_health_preg_i_illness,,radio,"Did you have any symptoms accompanying your first positive test for COVID-19?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 1",y,RH,,,,
+pex_bm_health_preg_i_illness_i_covid_004_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the date of your second positive test? {pex_bm_health_preg_i_illness_i_covid_004_i_01} {pex_bm_health_preg_i_illness_i_covid_004_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 2",,,,,,
+pex_bm_health_preg_i_illness_i_covid_004_i_01,pex_bm_health_preg_i_illness,,text,"What was the date of your second positive test?",,,date_mdy,,today,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 1 AND [pex_bm_health_preg_i_illness_i_covid_004_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_004_i_dk,pex_bm_health_preg_i_illness,,radio,"second date covid dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 1 AND [pex_bm_health_preg_i_illness_i_covid_004_i_01] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_004_i_02,pex_bm_health_preg_i_illness,,radio,"Did you have any symptoms accompanying your second positive test for COVID-19?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_i_covid_005_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the date of your third positive test? {pex_bm_health_preg_i_illness_i_covid_005_i_01} {pex_bm_health_preg_i_illness_i_covid_005_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 3",,,,,,
+pex_bm_health_preg_i_illness_i_covid_005_i_01,pex_bm_health_preg_i_illness,,text,"What was the date of your third positive test?",,,date_mdy,,today,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 3 AND [pex_bm_health_preg_i_illness_i_covid_005_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_005_i_dk,pex_bm_health_preg_i_illness,,radio,"third date covid dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 3 AND [pex_bm_health_preg_i_illness_i_covid_005_i_01] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_005_i_02,pex_bm_health_preg_i_illness,,radio,"Did you have any symptoms accompanying your third positive test for COVID-19?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_i_covid_006_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the date of your fourth positive test? {pex_bm_health_preg_i_illness_i_covid_006_i_01} {pex_bm_health_preg_i_illness_i_covid_006_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 4",,,,,,
+pex_bm_health_preg_i_illness_i_covid_006_i_01,pex_bm_health_preg_i_illness,,text,"What was the date of your fourth positive test?",,,date_mdy,,today,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 4 AND [pex_bm_health_preg_i_illness_i_covid_006_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_006_i_dk,pex_bm_health_preg_i_illness,,radio,"fourth date covid dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 4 AND [pex_bm_health_preg_i_illness_i_covid_006_i_01] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_006_i_02,pex_bm_health_preg_i_illness,,radio,"Did you have any symptoms accompanying your fourth positive test for COVID-19?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_i_covid_007_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the date of your fifth positive test? {pex_bm_health_preg_i_illness_i_covid_007_i_01} {pex_bm_health_preg_i_illness_i_covid_007_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 5",,,,,,
+pex_bm_health_preg_i_illness_i_covid_007_i_01,pex_bm_health_preg_i_illness,,text,"What was the date of your fifth positive test?",,,date_mdy,,today,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 5 AND [pex_bm_health_preg_i_illness_i_covid_007_i_dk] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_007_i_dk,pex_bm_health_preg_i_illness,,radio,"fifth date covid dk/decline","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 5 AND [pex_bm_health_preg_i_illness_i_covid_007_i_01] = ''",y,,,,,
+pex_bm_health_preg_i_illness_i_covid_007_i_02,pex_bm_health_preg_i_illness,,radio,"Did you have any symptoms accompanying your fifth positive test for COVID-19?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_i_covid_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_001,pex_bm_health_preg_i_illness,,radio,"Have you had any other illnesses since your last menstrual period on [screening_arm_1][setup_lmp] that we have not discussed?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,,,y,RH,,,,
+pex_bm_health_preg_i_illness_002_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many other illnesses have you had? {pex_bm_health_preg_i_illness_002} {pex_bm_health_preg_i_illness_002_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_001] = ""1"" ",,,,,,
+pex_bm_health_preg_i_illness_002,pex_bm_health_preg_i_illness,,dropdown,"How many other illnesses have you had? ","1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | 6, 6 | 7, 7 | 8, 8 | 9, 9 | 10, 10",,,,,,"[pex_bm_health_preg_i_illness_001] = ""1"" AND [pex_bm_health_preg_i_illness_002_i_dk] =''",y,,,,,
+pex_bm_health_preg_i_illness_002_i_dk,pex_bm_health_preg_i_illness,,radio,"illness number dk/decline
+","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_001] = ""1"" AND [pex_bm_health_preg_i_illness_002] =''",y,,,,,
+pex_bm_health_preg_i_illness_003_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of first illness (ICD-10) {pex_bm_health_preg_i_illness_003_i_01}
+{pex_bm_health_preg_i_illness_003_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 1",,,,,,
+pex_bm_health_preg_i_illness_003_i_01,pex_bm_health_preg_i_illness,,text,"Name of first illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 1 AND [pex_bm_health_preg_i_illness_003_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of first illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 1 AND [pex_bm_health_preg_i_illness_003_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_003_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_003_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 1",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_003_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_003_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_003_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_003_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_003_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_003_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_003_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_003_i_07,pex_bm_health_preg_i_illness,,text,"First illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_003_i_03] != """", [pex_bm_health_preg_i_illness_003_i_03], [pex_bm_health_preg_i_illness_003_i_05]))"
+pex_bm_health_preg_i_illness_003_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_003_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 1",,,,,,
+pex_bm_health_preg_i_illness_003_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_003_i_07] {pex_bm_health_preg_i_illness_003_i_09} {pex_bm_health_preg_i_illness_003_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_003_i_07] {pex_bm_health_preg_i_illness_003_i_10} {pex_bm_health_preg_i_illness_003_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 1",,,,,,
+pex_bm_health_preg_i_illness_003_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_003_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_003_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date 1 illness","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_003_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_003_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_003_i_09],today,,"[pex_bm_health_preg_i_illness_003_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date 1 illness","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_003_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_003_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 1",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_003_i_12} {pex_bm_health_preg_i_illness_003_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_003_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 1 ",,RH,,,,
+pex_bm_health_preg_i_illness_003_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,," [pex_bm_health_preg_i_illness_003_i_11] ='1' AND [pex_bm_health_preg_i_illness_003_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,,,,,
+pex_bm_health_preg_i_illness_003_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 1","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_003_i_11] ='1' AND [pex_bm_health_preg_i_illness_003_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_003_i_13_i_01} {pex_bm_health_preg_i_illness_003_i_13_i_02} {pex_bm_health_preg_i_illness_003_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_003_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 1 ",,RH,,,,
+pex_bm_health_preg_i_illness_003_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_003_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,,,,,
+pex_bm_health_preg_i_illness_003_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline duration fever 1","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_003_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,,
+pex_bm_health_preg_i_illness_003_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 1","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_003_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 1 ",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of second illness (ICD-10) {pex_bm_health_preg_i_illness_004_i_01}
+{pex_bm_health_preg_i_illness_004_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 2",,,,,,
+pex_bm_health_preg_i_illness_004_i_01,pex_bm_health_preg_i_illness,,text,"Name of second illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 2 AND [pex_bm_health_preg_i_illness_004_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of second illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 2 AND [pex_bm_health_preg_i_illness_004_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_004_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_004_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_004_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_004_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_004_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_004_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_004_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_004_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_004_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_004_i_07,pex_bm_health_preg_i_illness,,text,"second illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_004_i_03] != """", [pex_bm_health_preg_i_illness_004_i_03], [pex_bm_health_preg_i_illness_004_i_05]))"
+pex_bm_health_preg_i_illness_004_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_004_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 2",,,,,,
+pex_bm_health_preg_i_illness_004_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_004_i_07] {pex_bm_health_preg_i_illness_004_i_09} {pex_bm_health_preg_i_illness_004_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_004_i_07] {pex_bm_health_preg_i_illness_004_i_10} {pex_bm_health_preg_i_illness_004_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 2",,,,,,
+pex_bm_health_preg_i_illness_004_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_004_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,," [pex_bm_health_preg_i_illness_004_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 2","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_004_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_004_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_004_i_09],today,," [pex_bm_health_preg_i_illness_002] >= 2 AND [pex_bm_health_preg_i_illness_004_i_10_i_dk] = ''",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 2","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 2 AND [pex_bm_health_preg_i_illness_004_i_10] = ''",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_004_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_004_i_12} {pex_bm_health_preg_i_illness_004_i_12_i_dk}",,,,,,,"[pex_bm_health_preg_i_illness_004_i_11] = '1' AND [pex_bm_health_preg_i_illness_002] >= 2",,RH,,,,
+pex_bm_health_preg_i_illness_004_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_004_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 2",y,,,,,
+pex_bm_health_preg_i_illness_004_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 2","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_004_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_004_i_13_i_01} {pex_bm_health_preg_i_illness_004_i_13_i_02} {pex_bm_health_preg_i_illness_004_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_004_i_11] = '1' AND [pex_bm_health_preg_i_illness_002] >= 2",,RH,,,,
+pex_bm_health_preg_i_illness_004_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_004_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 2",y,,,,,
+pex_bm_health_preg_i_illness_004_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline fever duration 2","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_004_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_004_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of fever duration 2","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_004_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 2",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of third illness (ICD-10) {pex_bm_health_preg_i_illness_005_i_01}
+{pex_bm_health_preg_i_illness_005_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 3",,,,,,
+pex_bm_health_preg_i_illness_005_i_01,pex_bm_health_preg_i_illness,,text,"Name of third illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 3 AND [pex_bm_health_preg_i_illness_005_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of third illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 3 AND [pex_bm_health_preg_i_illness_005_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_005_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_005_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_005_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_005_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_005_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_005_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_005_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_005_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_005_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_005_i_07,pex_bm_health_preg_i_illness,,text,"third illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_005_i_03] != """", [pex_bm_health_preg_i_illness_005_i_03], [pex_bm_health_preg_i_illness_005_i_05]))"
+pex_bm_health_preg_i_illness_005_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_005_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 3",,,,,,
+pex_bm_health_preg_i_illness_005_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_005_i_07] {pex_bm_health_preg_i_illness_005_i_09} {pex_bm_health_preg_i_illness_005_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_005_i_07] {pex_bm_health_preg_i_illness_005_i_10} {pex_bm_health_preg_i_illness_005_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 3",,,,,,
+pex_bm_health_preg_i_illness_005_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_005_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_005_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline illness start date 3","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_005_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_005_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_005_i_09],today,,"[pex_bm_health_preg_i_illness_005_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline illness stop date 3 ","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_005_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_005_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_005_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_005_i_12} {pex_bm_health_preg_i_illness_005_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_005_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 3",,RH,,,,
+pex_bm_health_preg_i_illness_005_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_005_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 3",y,,,,,
+pex_bm_health_preg_i_illness_005_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 3","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_005_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_005_i_13_i_01} {pex_bm_health_preg_i_illness_005_i_13_i_02} {pex_bm_health_preg_i_illness_005_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_005_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 3",,RH,,,,
+pex_bm_health_preg_i_illness_005_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_005_i_13_i_dk] ='' AND [pex_bm_health_preg_i_illness_002] >= 3",y,,,,,
+pex_bm_health_preg_i_illness_005_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline fever duration 3","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_005_i_13_i_01] ='' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_005_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 3","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_005_i_13_i_dk] ='' AND [pex_bm_health_preg_i_illness_002] >= 3",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of fourth illness (ICD-10) {pex_bm_health_preg_i_illness_006_i_01}
+{pex_bm_health_preg_i_illness_006_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 4",,,,,,
+pex_bm_health_preg_i_illness_006_i_01,pex_bm_health_preg_i_illness,,text,"Name of fourth illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 4 AND [pex_bm_health_preg_i_illness_006_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of fourth illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 4 AND [pex_bm_health_preg_i_illness_006_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_006_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_006_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_006_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_006_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_006_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_006_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_006_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_006_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_006_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_006_i_07,pex_bm_health_preg_i_illness,,text,"fourth illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_006_i_03] != """", [pex_bm_health_preg_i_illness_006_i_03], [pex_bm_health_preg_i_illness_006_i_05]))"
+pex_bm_health_preg_i_illness_006_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_006_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 4",,,,,,
+pex_bm_health_preg_i_illness_006_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_006_i_07] {pex_bm_health_preg_i_illness_006_i_09} {pex_bm_health_preg_i_illness_006_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_006_i_07] {pex_bm_health_preg_i_illness_006_i_10} {pex_bm_health_preg_i_illness_006_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 4",,,,,,
+pex_bm_health_preg_i_illness_006_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_006_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_006_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 4","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_006_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_006_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_006_i_09],today,,"[pex_bm_health_preg_i_illness_006_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 4","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_006_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_006_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_006_i_12} {pex_bm_health_preg_i_illness_006_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_006_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 4",,RH,,,,
+pex_bm_health_preg_i_illness_006_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_006_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,,,,,
+pex_bm_health_preg_i_illness_006_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 4","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_006_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_006_i_13_i_01} {pex_bm_health_preg_i_illness_006_i_13_i_02} {pex_bm_health_preg_i_illness_006_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_006_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 4",,RH,,,,
+pex_bm_health_preg_i_illness_006_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_006_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,,,,,
+pex_bm_health_preg_i_illness_006_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline fever duration 4","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_006_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_006_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 4","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_006_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 4",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of fifth illness (ICD-10) {pex_bm_health_preg_i_illness_007_i_01}
+{pex_bm_health_preg_i_illness_007_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 5",,,,,,
+pex_bm_health_preg_i_illness_007_i_01,pex_bm_health_preg_i_illness,,text,"Name of fifth illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 5 AND [pex_bm_health_preg_i_illness_007_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of fifth illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 5 AND [pex_bm_health_preg_i_illness_007_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_007_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_007_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_007_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_007_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_007_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_007_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_007_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_007_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_007_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_007_i_07,pex_bm_health_preg_i_illness,,text,"fifth illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_007_i_03] != """", [pex_bm_health_preg_i_illness_007_i_03], [pex_bm_health_preg_i_illness_007_i_05]))"
+pex_bm_health_preg_i_illness_007_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_007_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 5",,,,,,
+pex_bm_health_preg_i_illness_007_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_007_i_07] {pex_bm_health_preg_i_illness_007_i_09} {pex_bm_health_preg_i_illness_007_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_007_i_07] {pex_bm_health_preg_i_illness_007_i_10} {pex_bm_health_preg_i_illness_007_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 5",,,,,,
+pex_bm_health_preg_i_illness_007_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_007_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_007_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 5","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_007_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_007_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_007_i_09],today,,"[pex_bm_health_preg_i_illness_007_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 5","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_007_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_007_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 5 AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_007_i_12} {pex_bm_health_preg_i_illness_007_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_007_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 5",,RH,,,,
+pex_bm_health_preg_i_illness_007_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_007_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,,,,,
+pex_bm_health_preg_i_illness_007_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 5","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_007_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_007_i_13_i_01} {pex_bm_health_preg_i_illness_007_i_13_i_02} {pex_bm_health_preg_i_illness_007_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_007_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 5",,RH,,,,
+pex_bm_health_preg_i_illness_007_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_007_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,,,,,
+pex_bm_health_preg_i_illness_007_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline fever duration 5","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_007_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_007_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 5","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_007_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 5",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of sixth illness (ICD-10) {pex_bm_health_preg_i_illness_008_i_01}
+{pex_bm_health_preg_i_illness_008_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 6",,,,,,
+pex_bm_health_preg_i_illness_008_i_01,pex_bm_health_preg_i_illness,,text,"Name of sixth illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 6 AND [pex_bm_health_preg_i_illness_008_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of sixth illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 6 AND [pex_bm_health_preg_i_illness_008_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_008_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_008_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_008_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_008_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_008_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_008_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_008_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_008_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_008_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_008_i_07,pex_bm_health_preg_i_illness,,text,"sixth illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_008_i_03] != """", [pex_bm_health_preg_i_illness_008_i_03], [pex_bm_health_preg_i_illness_008_i_05]))"
+pex_bm_health_preg_i_illness_008_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_008_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 6",,,,,,
+pex_bm_health_preg_i_illness_008_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_008_i_07] {pex_bm_health_preg_i_illness_008_i_09} {pex_bm_health_preg_i_illness_008_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_008_i_07] {pex_bm_health_preg_i_illness_008_i_10} {pex_bm_health_preg_i_illness_008_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 6",,,,,,
+pex_bm_health_preg_i_illness_008_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_008_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_008_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 6","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_008_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_008_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_008_i_09],today,,"[pex_bm_health_preg_i_illness_008_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 6","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_008_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_008_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_008_i_12} {pex_bm_health_preg_i_illness_008_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_008_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 6",,RH,,,,
+pex_bm_health_preg_i_illness_008_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_008_i_12_i_dk] ='' AND [pex_bm_health_preg_i_illness_002] >= 6",y,,,,,
+pex_bm_health_preg_i_illness_008_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 6","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_008_i_12] ='' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_008_i_13_i_01} {pex_bm_health_preg_i_illness_008_i_13_i_02} {pex_bm_health_preg_i_illness_008_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_008_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 6",,RH,,,,
+pex_bm_health_preg_i_illness_008_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_008_i_13_i_dk] ='' AND [pex_bm_health_preg_i_illness_002] >= 6",y,,,,,
+pex_bm_health_preg_i_illness_008_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline duration fever 6","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_008_i_13_i_01] ='' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_008_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 6","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_008_i_13_i_dk] ='' AND [pex_bm_health_preg_i_illness_002] >= 6",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of seventh illness (ICD-10) {pex_bm_health_preg_i_illness_009_i_01}
+{pex_bm_health_preg_i_illness_009_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 7",,,,,,
+pex_bm_health_preg_i_illness_009_i_01,pex_bm_health_preg_i_illness,,text,"Name of seventh illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 7 AND [pex_bm_health_preg_i_illness_009_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of seventh illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 7 AND [pex_bm_health_preg_i_illness_009_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_009_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_009_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_009_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_009_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_009_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_009_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_009_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_009_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_009_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_009_i_07,pex_bm_health_preg_i_illness,,text,"seventh illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_009_i_03] != """", [pex_bm_health_preg_i_illness_009_i_03], [pex_bm_health_preg_i_illness_009_i_05]))"
+pex_bm_health_preg_i_illness_009_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_009_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 7",,,,,,
+pex_bm_health_preg_i_illness_009_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_009_i_07] {pex_bm_health_preg_i_illness_009_i_09} {pex_bm_health_preg_i_illness_009_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_009_i_07] {pex_bm_health_preg_i_illness_009_i_10} {pex_bm_health_preg_i_illness_009_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 7",,,,,,
+pex_bm_health_preg_i_illness_009_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_009_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_009_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 7","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_009_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_009_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_009_i_09],today,,"[pex_bm_health_preg_i_illness_009_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 7","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_009_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_009_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_009_i_12} {pex_bm_health_preg_i_illness_009_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_009_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 7",,RH,,,,
+pex_bm_health_preg_i_illness_009_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_009_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,,,,,
+pex_bm_health_preg_i_illness_009_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 7","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_009_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_009_i_13_i_01} {pex_bm_health_preg_i_illness_009_i_13_i_02} {pex_bm_health_preg_i_illness_009_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_009_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 7",,RH,,,,
+pex_bm_health_preg_i_illness_009_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_009_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,,,,,
+pex_bm_health_preg_i_illness_009_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline duration fever 7","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_009_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_009_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 7","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_009_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 7",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of eighth illness (ICD-10) {pex_bm_health_preg_i_illness_010_i_01}
+{pex_bm_health_preg_i_illness_010_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 8",,,,,,
+pex_bm_health_preg_i_illness_010_i_01,pex_bm_health_preg_i_illness,,text,"Name of eighth illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 8 AND [pex_bm_health_preg_i_illness_010_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of eighth illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 8 AND [pex_bm_health_preg_i_illness_010_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_010_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_010_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_010_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_010_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_010_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_010_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_010_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_010_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_010_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_010_i_07,pex_bm_health_preg_i_illness,,text,"eighth illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_010_i_03] != """", [pex_bm_health_preg_i_illness_010_i_03], [pex_bm_health_preg_i_illness_010_i_05]))"
+pex_bm_health_preg_i_illness_010_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_010_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 8",,,,,,
+pex_bm_health_preg_i_illness_010_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_010_i_07] {pex_bm_health_preg_i_illness_010_i_09} {pex_bm_health_preg_i_illness_010_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_010_i_07] {pex_bm_health_preg_i_illness_010_i_10} {pex_bm_health_preg_i_illness_010_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 8",,,,,,
+pex_bm_health_preg_i_illness_010_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_010_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_010_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 8","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_010_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_010_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_010_i_09],today,,"[pex_bm_health_preg_i_illness_010_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 8","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_010_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_010_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_010_i_12} {pex_bm_health_preg_i_illness_010_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_010_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 8",,RH,,,,
+pex_bm_health_preg_i_illness_010_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_010_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,,,,,
+pex_bm_health_preg_i_illness_010_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp illness 8","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_010_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_010_i_13_i_01} {pex_bm_health_preg_i_illness_010_i_13_i_02} {pex_bm_health_preg_i_illness_010_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_010_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 8",,RH,,,,
+pex_bm_health_preg_i_illness_010_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_010_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,,,,,
+pex_bm_health_preg_i_illness_010_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline duration fever 8","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_010_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_010_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 8","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_010_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 8",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of ninth illness (ICD-10) {pex_bm_health_preg_i_illness_011_i_01}
+{pex_bm_health_preg_i_illness_011_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 9",,,,,,
+pex_bm_health_preg_i_illness_011_i_01,pex_bm_health_preg_i_illness,,text,"Name of ninth illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] >= 9 AND [pex_bm_health_preg_i_illness_011_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of ninth illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 9 AND [pex_bm_health_preg_i_illness_011_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_011_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_011_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_011_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_011_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_011_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_011_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_011_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_011_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_011_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_011_i_07,pex_bm_health_preg_i_illness,,text,"ninth illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_011_i_03] != """", [pex_bm_health_preg_i_illness_011_i_03], [pex_bm_health_preg_i_illness_011_i_05]))"
+pex_bm_health_preg_i_illness_011_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_011_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] >= 9",,,,,,
+pex_bm_health_preg_i_illness_011_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_011_i_07] {pex_bm_health_preg_i_illness_011_i_09} {pex_bm_health_preg_i_illness_011_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_011_i_07] {pex_bm_health_preg_i_illness_011_i_10} {pex_bm_health_preg_i_illness_011_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] >= 9",,,,,,
+pex_bm_health_preg_i_illness_011_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_011_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_011_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 9","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_011_i_09] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_011_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_011_i_09],today,,"[pex_bm_health_preg_i_illness_011_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 9","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_011_i_10] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_011_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_011_i_12} {pex_bm_health_preg_i_illness_011_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_011_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 9",,RH,,,,
+pex_bm_health_preg_i_illness_011_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_011_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,,,,,
+pex_bm_health_preg_i_illness_011_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 9","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_011_i_12] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_011_i_13_i_01} {pex_bm_health_preg_i_illness_011_i_13_i_02} {pex_bm_health_preg_i_illness_011_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_011_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] >= 9",,RH,,,,
+pex_bm_health_preg_i_illness_011_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_011_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,,,,,
+pex_bm_health_preg_i_illness_011_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline duration fever 9","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_011_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_011_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 9","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_011_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] >= 9",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_00,pex_bm_health_preg_i_illness,,descriptive,"Name of tenth illness (ICD-10) {pex_bm_health_preg_i_illness_012_i_01}
+{pex_bm_health_preg_i_illness_012_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] = 10",,,,,,
+pex_bm_health_preg_i_illness_012_i_01,pex_bm_health_preg_i_illness,,text,"Name of tenth illness (ICD-10)",BIOPORTAL:ICD10,,,,,," [pex_bm_health_preg_i_illness_002] = 10 AND [pex_bm_health_preg_i_illness_012_i_dk] =''",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_dk,pex_bm_health_preg_i_illness,,radio,"Name of tenth illness (ICD-10) -- Don't know","999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] = 10 AND [pex_bm_health_preg_i_illness_012_i_01] =''",y,,,,,
+pex_bm_health_preg_i_illness_012_i_02,pex_bm_health_preg_i_illness,,text,"If you don't know the name of the illness, please select the most prominent symptom.",BIOPORTAL:SYMP,,,,,,"[pex_bm_health_preg_i_illness_012_i_dk] = '999' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_03,pex_bm_health_preg_i_illness," ",sql,"Illness Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_012_i_01' and record = [record-name]) AND category='ICD10' order by label",,,,,," [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_012_i_04,pex_bm_health_preg_i_illness,,calc,"Select illness label","$('#pex_bm_health_preg_i_illness_012_i_03-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_012_i_05,pex_bm_health_preg_i_illness,,sql,"Symptom Label
+","SELECT distinct label from redcap_web_service_cache WHERE value in (SELECT value from redcap_data WHERE project_id = 57 and field_name = 'pex_bm_health_preg_i_illness_012_i_02' and record = [record-name]) AND category='SYMP' order by label",,,,,," [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_012_i_06,pex_bm_health_preg_i_illness,,calc,"Select symptom label","$('#pex_bm_health_preg_i_illness_012_i_05-tr select option:nth(1)').prop('selected',true)",,,,,," [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,," @HIDDEN"
+pex_bm_health_preg_i_illness_012_i_07,pex_bm_health_preg_i_illness,,text,"tenth illness or symptom",,,,,,," [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,," @HIDDEN @CALCTEXT(if([pex_bm_health_preg_i_illness_012_i_03] != """", [pex_bm_health_preg_i_illness_012_i_03], [pex_bm_health_preg_i_illness_012_i_05]))"
+pex_bm_health_preg_i_illness_012_i_08,pex_bm_health_preg_i_illness,,descriptive,"[pex_bm_health_preg_i_illness_012_i_07]
",,,,,,," [pex_bm_health_preg_i_illness_002] = 10",,,,,,
+pex_bm_health_preg_i_illness_012_i_09_i_00,pex_bm_health_preg_i_illness,,descriptive,"Start date of [pex_bm_health_preg_i_illness_012_i_07] {pex_bm_health_preg_i_illness_012_i_09} {pex_bm_health_preg_i_illness_012_i_09_i_dk} Stop date of [pex_bm_health_preg_i_illness_012_i_07] {pex_bm_health_preg_i_illness_012_i_10} {pex_bm_health_preg_i_illness_012_i_10_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_002] = 10",,,,,,
+pex_bm_health_preg_i_illness_012_i_09,pex_bm_health_preg_i_illness,,text,"Start date of [pex_bm_health_preg_i_illness_012_i_07] ",,,date_mdy,[screening_arm_1][setup_lmp],today,,"[pex_bm_health_preg_i_illness_012_i_09_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_09_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline start date illness 10","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_012_i_09] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_10,pex_bm_health_preg_i_illness,,text,"Stop date of [pex_bm_health_preg_i_illness_012_i_07]",,,date_mdy,[pex_bm_health_preg_i_illness_012_i_09],today,,"[pex_bm_health_preg_i_illness_012_i_10_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_10_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline stop date illness 10","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_012_i_10] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_11,pex_bm_health_preg_i_illness,,radio,"Did you have a fever with [pex_bm_health_preg_i_illness_012_i_07]?","1, Yes | 0, No | 999, Don't know | 777, Decline to answer",,,,,," [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_12_i_00,pex_bm_health_preg_i_illness,,descriptive,"What was the highest temperature of the fever? {pex_bm_health_preg_i_illness_012_i_12} {pex_bm_health_preg_i_illness_012_i_12_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_012_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] = 10",,RH,,,,
+pex_bm_health_preg_i_illness_012_i_12,pex_bm_health_preg_i_illness,,text,"What was the highest temperature of the fever?",,,number,98.6,108,,"[pex_bm_health_preg_i_illness_012_i_12_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,,,,,
+pex_bm_health_preg_i_illness_012_i_12_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline temp 10","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_012_i_12] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_13_i_00,pex_bm_health_preg_i_illness,,descriptive,"How many hours or days did the fever last? {pex_bm_health_preg_i_illness_012_i_13_i_01} {pex_bm_health_preg_i_illness_012_i_13_i_02} {pex_bm_health_preg_i_illness_012_i_13_i_dk}",,,,,,," [pex_bm_health_preg_i_illness_012_i_11] ='1' AND [pex_bm_health_preg_i_illness_002] = 10",,RH,,,,
+pex_bm_health_preg_i_illness_012_i_13_i_01,pex_bm_health_preg_i_illness,,text,"How many hours or days did the fever last?",,,number,,,,"[pex_bm_health_preg_i_illness_012_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,,,,,
+pex_bm_health_preg_i_illness_012_i_13_i_dk,pex_bm_health_preg_i_illness,,radio,"dk/decline fever duration 10","999, Don't know | 777, Decline to answer",,,,,,"[pex_bm_health_preg_i_illness_012_i_13_i_01] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
+pex_bm_health_preg_i_illness_012_i_13_i_02,pex_bm_health_preg_i_illness,,radio,"Unit of duration fever 10","0, Hours | 1, Days",,,,,,"[pex_bm_health_preg_i_illness_012_i_13_i_dk] = '' AND [pex_bm_health_preg_i_illness_002] = 10",y,RH,,,,
diff --git a/reproschema/tests/test_rs2redcap_redcap2rs.py b/reproschema/tests/test_rs2redcap_redcap2rs.py
index c953cab..74ca4c7 100644
--- a/reproschema/tests/test_rs2redcap_redcap2rs.py
+++ b/reproschema/tests/test_rs2redcap_redcap2rs.py
@@ -1,7 +1,6 @@
-import csv
import os
from pathlib import Path
-from shutil import copytree, rmtree
+from shutil import copytree
import pytest
from click.testing import CliRunner
@@ -11,7 +10,7 @@
from ..jsonldutils import _is_url, load_file
from ..models import Activity, Item, Protocol, ResponseOption
from ..redcap2reproschema import normalize_condition
-from ..utils import fixing_old_schema, start_server, stop_server
+from ..utils import start_server, stop_server
def create_protocol_dict(
@@ -182,7 +181,9 @@ def compare_protocols(prot_tree_orig, prot_tree_final):
):
errors_list.append(error_shortmsg)
else: # differences only in the "_schema suffix
- warnings_list.append(error_shortmsg)
+ warnings_list.append(
+ error_shortmsg + ", but only differ in the _schema suffix"
+ )
# check order
act_order_orig = [
@@ -204,27 +205,13 @@ def compare_protocols(prot_tree_orig, prot_tree_final):
act_props_final = {
el.variableName: el for el in act_final.ui.addProperties
}
- # issues with these schema reprorted in the reproschema-library
- known_issues_nm = [
- "dsm_5_parent_guardian_rated_level_1_crosscutting_s_schema_first_19",
- "dsm_5_parent_guardian_rated_level_1_crosscutting_s_schema_20_to_25",
- "RCADS25_caregiver_administered_schema",
- "RCADS25_youth_administered_schema",
- "DSM5_crosscutting_youth_schema",
- ]
+
if act_props_orig.keys() != act_props_final.keys():
- if act_name in known_issues_nm:
- warnings_list.append(
- print_return_msg(
- f"Activity {act_name}: addProperties have different elements"
- )
- )
- else:
- errors_list.append(
- print_return_msg(
- f"Activity {act_name}: addProperties have different elements, orig: {act_props_orig} and final: {act_props_final}"
- )
+ errors_list.append(
+ print_return_msg(
+ f"Activity {act_name}: addProperties have different elements, orig: {act_props_orig} and final: {act_props_final}"
)
+ )
else:
for nm, el in act_props_final.items():
for key in ["isVis", "valueRequired"]:
@@ -281,18 +268,11 @@ def compare_protocols(prot_tree_orig, prot_tree_final):
act_comp_orig = {el.variableName: el for el in act_orig.compute}
act_comp_final = {el.variableName: el for el in act_final.compute}
if act_comp_final.keys() != act_comp_orig.keys():
- if act_name in known_issues_nm:
- warnings_list.append(
- print_return_msg(
- f"Activity {act_name}: compute have different elements"
- )
- )
- else:
- errors_list.append(
- print_return_msg(
- f"Activity {act_name}: compute have different elements, orig: {act_comp_orig}, final: {act_comp_final}"
- )
+ errors_list.append(
+ print_return_msg(
+ f"Activity {act_name}: compute have different elements, orig: {act_comp_orig}, final: {act_comp_final}"
)
+ )
else:
for nm, el in act_comp_final.items():
if normalize_condition(
@@ -308,18 +288,11 @@ def compare_protocols(prot_tree_orig, prot_tree_final):
# check items:
if act_items_final.keys() != act_items_orig.keys():
- if act_name in known_issues_nm:
- warnings_list.append(
- print_return_msg(
- f"Activity {act_name}: items have different elements"
- )
- )
- else:
- errors_list.append(
- print_return_msg(
- f"Activity {act_name}: items have different elements, orig: {act_items_orig}, final: {act_items_final}"
- )
+ errors_list.append(
+ print_return_msg(
+ f"Activity {act_name}: items have different elements, orig: {act_items_orig}, final: {act_items_final}"
)
+ )
else:
for nm, el in act_items_final.items():
if (
@@ -375,11 +348,14 @@ def compare_protocols(prot_tree_orig, prot_tree_final):
# check response options
respopt_orig = act_items_orig[nm]["obj"].responseOptions
respopt_final = el["obj"].responseOptions
+
# TODO: min val does not work
# TODO: check choices
# for key in ["minValue", "maxValue"]:
# if getattr(respopt_final, key) != getattr(respopt_orig, key):
# errors_list.append(print(f"Activity {act_name}: items {nm} have different {key}"))
+ print("Warnings: ", "check min/max values and choices not implemented")
+ warnings_list.append("TODO: check min/max values and choices")
return errors_list, warnings_list
@@ -440,6 +416,5 @@ def test_rs2redcap_redcap2rs(tmpdir):
errors_list, warnings_list = compare_protocols(
prot_tree_orig, prot_tree_final
)
-
assert not errors_list, f"Errors: {errors_list}"
print("No errors, but found warnings: ", warnings_list)