FDA Submission Workflow
This guide walks through creating FDA-compliant XPT files for regulatory submissions.
Prerequisites
- Understanding of CDISC SDTM/ADaM standards
- Access to define.xml for your study
- Clinical trial data in a structured format
Step 1: Design Your Dataset
Plan your dataset structure based on SDTM/ADaM:
// Example: Adverse Events (AE) domain
// Required SDTM variables: STUDYID, DOMAIN, USUBJID, AESEQ, AETERM, ...
use xportrs::{Column, ColumnData, Dataset, Format, VariableRole};Step 2: Create the Dataset with Full Metadata
use xportrs::{Column, ColumnData, Dataset, Format, VariableRole};
struct YourDataSource { studyid: Vec<Option<String>>, usubjid: Vec<Option<String>>, aeseq: Vec<Option<f64>>, aeterm: Vec<Option<String>>, aedecod: Vec<Option<String>>, aesev: Vec<Option<String>>, aestdtc: Vec<Option<String>>, aeendtc: Vec<Option<String>> }
impl YourDataSource { fn len(&self) -> usize { self.studyid.len() } }
fn create_ae_dataset(data: &YourDataSource) -> xportrs::Result<Dataset> {
let dataset = Dataset::with_label("AE", "Adverse Events", vec![
// Identifier variables
Column::with_role(
"STUDYID",
VariableRole::Identifier,
ColumnData::String(data.studyid.clone()),
)
.with_label("Study Identifier")
.with_format(Format::character(20)),
Column::new("DOMAIN", ColumnData::String(
vec![Some("AE".into()); data.len()]
))
.with_label("Domain Abbreviation")
.with_format(Format::character(2))
.with_length(2),
Column::with_role(
"USUBJID",
VariableRole::Identifier,
ColumnData::String(data.usubjid.clone()),
)
.with_label("Unique Subject Identifier")
.with_format(Format::character(40)),
Column::with_role(
"AESEQ",
VariableRole::Topic,
ColumnData::F64(data.aeseq.clone()),
)
.with_label("Sequence Number")
.with_format(Format::numeric(8, 0)),
// Qualifier variables
Column::with_role(
"AETERM",
VariableRole::Qualifier,
ColumnData::String(data.aeterm.clone()),
)
.with_label("Reported Term for the Adverse Event")
.with_format(Format::character(200))
.with_length(200),
Column::new("AEDECOD", ColumnData::String(data.aedecod.clone()))
.with_label("Dictionary-Derived Term")
.with_format(Format::character(200))
.with_length(200),
Column::new("AESEV", ColumnData::String(data.aesev.clone()))
.with_label("Severity/Intensity")
.with_format(Format::character(10))
.with_length(10),
// Timing variables
Column::with_role(
"AESTDTC",
VariableRole::Timing,
ColumnData::String(data.aestdtc.clone()),
)
.with_label("Start Date/Time of Adverse Event")
.with_format(Format::character(19))
.with_length(19),
Column::new("AEENDTC", ColumnData::String(data.aeendtc.clone()))
.with_label("End Date/Time of Adverse Event")
.with_format(Format::character(19))
.with_length(19),
])?;
Ok(dataset)
}Step 3: Validate for FDA Compliance
use xportrs::{Agency, Dataset, Severity, Xpt};
fn validate_for_fda(dataset: Dataset) -> xportrs::Result<xportrs::ValidatedWrite> {
let validated = Xpt::writer(dataset)
.agency(Agency::FDA)
.finalize()?;
// Report all issues
println!("Validation Results:");
println!(" Errors: {}", validated.issues().iter()
.filter(|i| i.severity() == Severity::Error).count());
println!(" Warnings: {}", validated.issues().iter()
.filter(|i| i.severity() == Severity::Warning).count());
// Detail issues
for issue in validated.issues() {
let prefix = match issue.severity() {
Severity::Error => "ERROR",
Severity::Warning => "WARN",
Severity::Info => "INFO",
};
println!(" [{}] {}: {}", prefix, issue.target(), issue);
}
// Fail on errors
if validated.has_errors() {
return Err(xportrs::Error::invalid_data(
"FDA validation failed with errors"
));
}
Ok(validated)
}Step 4: Write the XPT File
use std::path::Path;
fn write_submission_file(
validated: xportrs::ValidatedWrite,
output_dir: &Path,
) -> xportrs::Result<()> {
let output_path = output_dir.join("ae.xpt");
// Write (may split if >5GB)
let paths = validated.write_path(&output_path)?;
for path in &paths {
println!("Wrote: {}", path.display());
// Verify file size
let size = std::fs::metadata(path)?.len();
println!(" Size: {} bytes ({:.2} GB)",
size, size as f64 / 1_073_741_824.0);
}
Ok(())
}Step 5: Verify the Output
use xportrs::Xpt;
fn verify_output(path: &str) -> xportrs::Result<()> {
// Read back
let dataset = Xpt::read(path)?;
// Verify structure
println!("\nVerification:");
println!(" Domain: {}", dataset.domain_code());
println!(" Label: {:?}", dataset.dataset_label());
println!(" Rows: {}", dataset.nrows());
println!(" Columns: {}", dataset.ncols());
// Check metadata preserved
for col in dataset.columns() {
print!(" {} ", col.name());
if col.label().is_some() { print!("[label] "); }
if col.format().is_some() { print!("[format] "); }
if col.explicit_length().is_some() { print!("[length] "); }
println!();
}
Ok(())
}Complete Example
use xportrs::{Agency, Column, ColumnData, Dataset, Format, Severity, Xpt};
use std::path::PathBuf;
fn main() -> xportrs::Result<()> {
fn create_submission() -> xportrs::Result<()> {
// 1. Create dataset
let dataset = Dataset::with_label("AE", "Adverse Events", vec![
Column::new("STUDYID", ColumnData::String(vec![
Some("ABC-123".into()),
Some("ABC-123".into()),
]))
.with_label("Study Identifier")
.with_format(Format::character(20)),
Column::new("DOMAIN", ColumnData::String(vec![
Some("AE".into()),
Some("AE".into()),
]))
.with_label("Domain Abbreviation")
.with_format(Format::character(2)),
Column::new("USUBJID", ColumnData::String(vec![
Some("ABC-123-001".into()),
Some("ABC-123-002".into()),
]))
.with_label("Unique Subject Identifier")
.with_format(Format::character(40)),
Column::new("AESEQ", ColumnData::F64(vec![
Some(1.0),
Some(1.0),
]))
.with_label("Sequence Number"),
Column::new("AETERM", ColumnData::String(vec![
Some("HEADACHE".into()),
Some("NAUSEA".into()),
]))
.with_label("Reported Term for the Adverse Event")
.with_format(Format::character(200))
.with_length(200),
Column::new("AESTDTC", ColumnData::String(vec![
Some("2024-01-15".into()),
Some("2024-01-16".into()),
]))
.with_label("Start Date/Time of Adverse Event")
.with_format(Format::character(19)),
])?;
// 2. Validate for FDA
let validated = Xpt::writer(dataset)
.agency(Agency::FDA)
.finalize()?;
// 3. Report issues
if !validated.issues().is_empty() {
println!("Validation Issues:");
for issue in validated.issues() {
println!(" [{}] {}", issue.severity(), issue);
}
}
// 4. Check for blocking errors
if validated.has_errors() {
eprintln!("Cannot proceed due to validation errors");
return Err(xportrs::Error::invalid_data("Validation failed"));
}
// 5. Write file
let output = PathBuf::from("output/ae.xpt");
std::fs::create_dir_all(output.parent().unwrap())?;
validated.write_path(&output)?;
// 6. Verify
let loaded = Xpt::read(&output)?;
assert_eq!(loaded.domain_code(), "AE");
assert_eq!(loaded.nrows(), 2);
println!("\nSuccessfully created ae.xpt for FDA submission");
Ok(())
}
Ok(())
}Checklist
Before submission, verify:
- Dataset name ≤8 characters, uppercase
- Variable names ≤8 characters, uppercase
- Variable labels ≤40 characters, ASCII only
- Character variables ≤200 bytes
- All variables have labels
- Dataset has a label
- File size ≤5GB (or properly split)
- Pinnacle 21 validation passed
- Labels match define.xml
Common Issues
Missing Labels
[WARN] MYVAR: Variable 'MYVAR' is missing a label
Fix: Add .with_label("...") to all columns.
Non-ASCII Characters
[ERROR] AETERM: Variable label contains non-ASCII characters
Fix: Replace accented characters (é→e, ñ→n) and special symbols.
Variable Name Too Long
[ERROR] MYLONGNAME: Variable name exceeds 8 bytes
Fix: Shorten variable names to ≤8 characters.
Next Steps
- Run Pinnacle 21 validation on generated files
- Verify define.xml consistency
- Package with eCTD structure