///|
fn html_escape(value : String) -> String {
  let output = StringBuilder()
  for character in value.to_array() {
    match character {
      '&' => output.write_string("&")
      '<' => output.write_string("<")
      '>' => output.write_string(">")
      '"' => output.write_string(""")
      '\'' => output.write_string("'")
      _ => output.write_char(character)
    }
  }
  output.to_string()
}

///|
fn html_status_class(status : @evidence.AssessmentStatus) -> String {
  match status {
    @evidence.InControl => "in-control"
    @evidence.Warning => "warning"
    @evidence.RequiresReview => "requires-review"
    @evidence.Incomplete => "incomplete"
  }
}

///|
fn html_find_run(runs : Array[@run.QCRun], run_index : Int) -> @run.QCRun? {
  runs.get(run_index)
}

///|
fn html_find_first_assessment(
  trajectory : @evidence.Trajectory,
  status : @evidence.AssessmentStatus,
) -> Int? {
  for index, assessment in trajectory.assessments {
    if assessment.status == status {
      return Some(index)
    }
  }
  None
}

///|
fn html_find_epoch_run_index(
  runs : Array[@run.QCRun],
  epoch : @epoch.QCEpoch,
) -> Int? {
  for index, run in runs {
    if run.epoch.has_same_metadata(epoch) {
      return Some(index)
    }
  }
  None
}

///|
fn html_find_evidence_run_index(
  runs : Array[@run.QCRun],
  evidence : @evidence.EvidencePoint,
) -> Int? {
  for index, run in runs {
    if run.run_id == evidence.run_id &&
      run.sequence == evidence.sequence &&
      run.epoch.id == evidence.epoch_id {
      return Some(index)
    }
  }
  None
}

///|
fn html_find_control_rule_run_index(
  trajectory : @evidence.Trajectory,
  control_level_id : String,
  rule : @assay.Rule,
) -> Int? {
  for index, assessment in trajectory.assessments {
    for hit in assessment.hits {
      if hit.rule == rule {
        for point in hit.evidence {
          if point.control_level_id == control_level_id {
            return Some(index)
          }
        }
      }
    }
  }
  None
}

///|
fn html_find_epoch_control_rule_run_index(
  runs : Array[@run.QCRun],
  trajectory : @evidence.Trajectory,
  epoch : @epoch.QCEpoch,
  control_level_id : String,
  rule : @assay.Rule,
) -> Int? {
  for index, assessment in trajectory.assessments {
    match runs.get(index) {
      Some(run) if run.epoch.has_same_metadata(epoch) =>
        for hit in assessment.hits {
          if hit.rule == rule {
            for point in hit.evidence {
              if point.control_level_id == control_level_id {
                return Some(index)
              }
            }
          }
        }
      _ => ()
    }
  }
  None
}

///|
fn html_find_coverage_gap_run_index(
  runs : Array[@run.QCRun],
  trajectory : @evidence.Trajectory,
  coverage : ControlCoverageCount,
  precision : Int,
) -> Int? {
  for index, run in runs {
    if run.epoch.has_same_metadata(coverage.epoch) &&
      trajectory.assessments.get(index) is Some(_) {
      let mut point : @run.ControlPoint? = None
      for observation in run.observations {
        if observation.control_level_id == coverage.control_level_id &&
          point is None {
          point = Some(observation)
        }
      }
      if coverage.missing_runs > 0 && point is None {
        return Some(index)
      }
      if coverage.missing_runs == 0 &&
        coverage.precision_mismatch_runs > 0 &&
        point is Some(observation) &&
        observation.precision != precision {
        return Some(index)
      }
    }
  }
  None
}

///|
fn html_append_status_card(
  output : StringBuilder,
  label : String,
  count : Int,
  status : @evidence.AssessmentStatus,
  trajectory : @evidence.Trajectory,
) -> Unit {
  output.write_string("
")
  match html_find_first_assessment(trajectory, status) {
    Some(index) => {
      output.write_string("")
    }
    None => ()
  }
  output.write_string(label)
  output.write_string("")
  output.write_string(count.to_string())
  output.write_string("")
  match html_find_first_assessment(trajectory, status) {
    Some(_) => output.write_string("")
    None => ()
  }
  output.write_string("
\n")
}

///|
fn html_append_evidence(
  output : StringBuilder,
  evidence : @evidence.EvidencePoint,
  runs : Array[@run.QCRun],
) -> Unit {
  output.write_string("")
  match html_find_evidence_run_index(runs, evidence) {
    Some(index) => {
      output.write_string("")
      output.write_string(html_escape(evidence.run_id))
      output.write_string("")
    }
    None => output.write_string(html_escape(evidence.run_id))
  }
  output.write_string(
    "" +
    html_escape(evidence.control_level_id) +
    "" +
    format_scaled(evidence.value, evidence.precision) +
    " " +
    html_escape(evidence.unit) +
    "" +
    format_scaled(evidence.mean, evidence.precision) +
    "" +
    format_scaled(evidence.standard_deviation, evidence.precision) +
    "" +
    format_scaled(evidence.threshold, evidence.precision) +
    "" +
    direction_name(evidence.direction) +
    "\n",
  )
}

///|
fn html_append_assessment(
  output : StringBuilder,
  program : @assay.AssayProgram,
  run_index : Int,
  assessment : @evidence.RunAssessment,
  runs : Array[@run.QCRun],
) -> Unit {
  output.write_string("
")
  output.write_string(assessment.status.name())
  output.write_string("Run ")
  output.write_string(html_escape(assessment.run_id))
  output.write_string("sequence ")
  output.write_string(assessment.sequence.to_string())
  output.write_string("
\n")
  match html_find_run(runs, run_index) {
    Some(run) => {
      output.write_string("
Timestamp
")
      output.write_string(html_escape(run.timestamp))
      output.write_string("
Epoch
")
      output.write_string(html_escape(run.epoch.id))
      output.write_string("
Reagent lot
")
      output.write_string(html_escape(run.epoch.reagent_lot))
      output.write_string("
Control lot
")
      output.write_string(html_escape(run.epoch.control_lot))
      output.write_string("
Calibration
")
      output.write_string(html_escape(run.epoch.calibration_id))
      output.write_string("
Program version
")
      output.write_string(html_escape(run.epoch.program_version))
      output.write_string("
\n")
      output.write_string(
        "
Observations
\n\n",
      )
      if run.observations.length() == 0 {
        output.write_string("\n")
      } else {
        for point in run.observations {
          output.write_string(
            "\n",
          )
        }
      }
      output.write_string("
ControlValuePrecision
No observations
" +
            html_escape(point.control_level_id) +
            "" +
            format_scaled(point.value, point.precision) +
            " " +
            html_escape(program.unit) +
            "" +
            point.precision.to_string() +
            "
\n")
    }
    None => output.write_string("
Run snapshot unavailable.
\n")
  }
  if assessment.hits.length() == 0 {
    output.write_string("
No rule hits.
\n")
  } else {
    output.write_string("
Rule signals and evidence
\n")
    for hit in assessment.hits {
      output.write_string("
")
      output.write_string(hit.rule.name())
      output.write_string(" ")
      output.write_string(scope_name(hit.scope))
      output.write_string("
")
      output.write_string(html_escape(hit.reason))
      output.write_string("
\n")
      if hit.evidence.length() > 0 {
        output.write_string(
          "\n",
        )
        for evidence in hit.evidence {
          html_append_evidence(output, evidence, runs)
        }
        output.write_string("
RunControlObservedMeanSDThreshold distanceDirection
\n")
      }
      output.write_string("
\n")
    }
  }
  for issue in assessment.input_issues {
    output.write_string("
Input issue [")
    output.write_string(issue.code.name())
    output.write_string("]: ")
    output.write_string(html_escape(issue.message))
    output.write_string("
\n")
  }
  output.write_string("
\n")
}

///|
/// Render a deterministic, self-contained HTML audit report with an embedded
/// Levey–Jennings chart. The document has no scripts, external styles, or
/// network dependencies and can be opened offline.
pub fn render_audit_html(
  program : @assay.AssayProgram,
  runs : Array[@run.QCRun],
  trajectory : @evidence.Trajectory,
) -> String {
  let summary = audit_summary(program, runs, trajectory)
  let output = StringBuilder()
  output.write_string(
    "\n\nQC audit report — ",
  )
  output.write_string(html_escape(program.assay_id))
  output.write_string("
\n
Offline QC audit report · schema version 1
",
  )
  output.write_string(html_escape(program.assay_id))
  output.write_string("
Measurement unit: ")
  output.write_string(html_escape(program.unit))
  output.write_string(" · Decimal precision: ")
  output.write_string(program.precision.to_string())
  output.write_string("
\n")

  output.write_string(
    "
Summary
\n",
  )
  output.write_string("
Input runs")
  output.write_string(summary.input_runs.to_string())
  output.write_string(
    "
Assessed runs",
  )
  output.write_string(summary.assessed_runs.to_string())
  output.write_string("
\n")
  html_append_status_card(
    output,
    "In control",
    summary.in_control,
    @evidence.InControl,
    trajectory,
  )
  html_append_status_card(
    output,
    "Warning",
    summary.warning,
    @evidence.Warning,
    trajectory,
  )
  html_append_status_card(
    output,
    "Requires review",
    summary.requires_review,
    @evidence.RequiresReview,
    trajectory,
  )
  html_append_status_card(
    output,
    "Incomplete",
    summary.incomplete,
    @evidence.Incomplete,
    trajectory,
  )
  output.write_string("
Rule hits")
  output.write_string(summary.total_rule_hits.to_string())
  output.write_string("
Track issues")
  output.write_string(summary.track_issues.to_string())
  output.write_string("
Rule hit counts
\n")
  if summary.total_rule_hits == 0 {
    output.write_string("
No rule hits.
\n")
  } else {
    output.write_string(
      "\n",
    )
    for hit in summary.rule_hits {
      if hit.count > 0 {
        output.write_string("\n")
      }
    }
    output.write_string("
RuleCountDisposition
")
        output.write_string(hit.rule.name())
        output.write_string("")
        output.write_string(hit.count.to_string())
        output.write_string("")
        output.write_string(
          audit_rule_disposition_name(program.disposition_for(hit.rule)),
        )
        output.write_string("
\n")
  }
  output.write_string("
Control rule hit counts
\n")
  if summary.control_rule_hits.length() == 0 {
    output.write_string("
No control-level rule hits.
\n")
  } else {
    output.write_string(
      "\n",
    )
    for entry in summary.control_rule_hits {
      output.write_string("\n")
    }
    output.write_string("
ControlRuleHit runsNavigate
")
      output.write_string(html_escape(entry.control_level_id))
      output.write_string("")
      output.write_string(entry.rule.name())
      output.write_string("")
      output.write_string(entry.count.to_string())
      output.write_string("")
      match
        html_find_control_rule_run_index(
          trajectory,
          entry.control_level_id,
          entry.rule,
        ) {
        Some(index) => {
          output.write_string("Open first signal")
        }
        None => output.write_string("No evidence run")
      }
      output.write_string("
\n")
  }
  output.write_string("
Rule signals by epoch and control
\n")
  if summary.epoch_control_rule_hits.length() == 0 {
    output.write_string(
      "
No epoch-specific control rule hits.
\n",
    )
  } else {
    output.write_string(
      "\n",
    )
    for entry in summary.epoch_control_rule_hits {
      output.write_string("\n")
    }
    output.write_string("
EpochControlRuleHit runsDispositionNavigate
")
      output.write_string(html_escape(entry.epoch.id))
      output.write_string("")
      output.write_string(html_escape(entry.control_level_id))
      output.write_string("")
      output.write_string(entry.rule.name())
      output.write_string("")
      output.write_string(entry.count.to_string())
      output.write_string("")
      output.write_string(
        audit_rule_disposition_name(program.disposition_for(entry.rule)),
      )
      output.write_string("")
      match
        html_find_epoch_control_rule_run_index(
          runs,
          trajectory,
          entry.epoch,
          entry.control_level_id,
          entry.rule,
        ) {
        Some(index) => {
          output.write_string("Open first signal")
        }
        None => output.write_string("No evidence run")
      }
      output.write_string("
\n")
  }
  output.write_string("
Control observation coverage
\n")
  if summary.control_coverage.length() == 0 {
    output.write_string(
      "
No expected control observations.
\n",
    )
  } else {
    output.write_string(
      "\n",
    )
    for coverage in summary.control_coverage {
      output.write_string("\n")
    }
    output.write_string("
EpochControlRequiredExpected runsObserved runsMissing runsPrecision mismatchNavigate
")
      output.write_string(html_escape(coverage.epoch.id))
      output.write_string("")
      output.write_string(html_escape(coverage.control_level_id))
      output.write_string("")
      output.write_string(if coverage.required { "Yes" } else { "No" })
      output.write_string("")
      output.write_string(coverage.expected_runs.to_string())
      output.write_string("")
      output.write_string(coverage.observed_runs.to_string())
      output.write_string("")
      output.write_string(coverage.missing_runs.to_string())
      output.write_string("")
      output.write_string(coverage.precision_mismatch_runs.to_string())
      output.write_string("")
      match
        html_find_coverage_gap_run_index(
          runs,
          trajectory,
          coverage,
          program.precision,
        ) {
        Some(index) => {
          output.write_string("")
          output.write_string(
            if coverage.missing_runs > 0 {
              "Open first missing run"
            } else {
              "Open first precision mismatch"
            },
          )
          output.write_string("")
        }
        None => output.write_string("No coverage gaps")
      }
      output.write_string("
\n")
  }
  output.write_string("
\n")

  output.write_string(
    "
Assay configuration
Program: ",
  )
  output.write_string(html_escape(program.assay_id))
  output.write_string("; unit: ")
  output.write_string(html_escape(program.unit))
  output.write_string("; precision: ")
  output.write_string(program.precision.to_string())
  output.write_string(
    "
\n",
  )
  for level in program.levels {
    output.write_string("\n")
  }
  output.write_string("
ControlMeanStandard deviationRequired
")
    output.write_string(html_escape(level.id))
    output.write_string("")
    output.write_string(format_scaled(level.mean, program.precision))
    output.write_string("")
    output.write_string(
      format_scaled(level.standard_deviation, program.precision),
    )
    output.write_string("")
    output.write_string(if level.required { "Yes" } else { "No" })
    output.write_string("
Rule dispositions
\n")
  output.write_string(
    "\n",
  )
  for rule in audit_rule_order() {
    output.write_string("\n")
  }
  output.write_string("
RuleDisposition
")
    output.write_string(rule.name())
    output.write_string("")
    output.write_string(
      audit_rule_disposition_name(program.disposition_for(rule)),
    )
    output.write_string("
QC epochs
\n")
  if summary.epoch_runs.length() == 0 {
    output.write_string("
No epochs.
\n")
  } else {
    output.write_string(
      "\n",
    )
    for entry in summary.epoch_runs {
      output.write_string("\n")
    }
    output.write_string("
EpochReagent lotControl lotCalibrationProgram versionRunsIn controlWarningRequires reviewIncompleteRule hitsNavigate
")
      output.write_string(html_escape(entry.epoch.id))
      output.write_string("")
      output.write_string(html_escape(entry.epoch.reagent_lot))
      output.write_string("")
      output.write_string(html_escape(entry.epoch.control_lot))
      output.write_string("")
      output.write_string(html_escape(entry.epoch.calibration_id))
      output.write_string("")
      output.write_string(html_escape(entry.epoch.program_version))
      output.write_string("")
      output.write_string(entry.count.to_string())
      output.write_string("")
      output.write_string(entry.in_control.to_string())
      output.write_string("")
      output.write_string(entry.warning.to_string())
      output.write_string("")
      output.write_string(entry.requires_review.to_string())
      output.write_string("")
      output.write_string(entry.incomplete.to_string())
      output.write_string("")
      output.write_string(
        audit_epoch_total_rule_hits(summary.epoch_rule_hits, entry.epoch).to_string(),
      )
      output.write_string("")
      match html_find_epoch_run_index(runs, entry.epoch) {
        Some(index) => {
          output.write_string("Open first run")
        }
        None => output.write_string("No run detail")
      }
      output.write_string("
\n")
  }
  output.write_string("
\n")

  output.write_string(
    "
Levey–Jennings chart
",
  )
  output.write_string(render_levey_jennings_svg(program, runs, trajectory))
  output.write_string(
    "
Control observations, target mean, ±1/2/3 SD lines, epoch boundaries, and rule evidence.
\n",
  )

  output.write_string("
Run assessments
")
  if trajectory.assessments.length() == 0 {
    output.write_string("
No run assessments.
\n")
  } else {
    for index, assessment in trajectory.assessments {
      html_append_assessment(output, program, index, assessment, runs)
    }
  }
  output.write_string("
\n")

  if trajectory.input_issues.length() > 0 {
    output.write_string("
Track issues
\n")
    for issue in trajectory.input_issues {
      output.write_string("
")
      output.write_string(issue.code.name())
      output.write_string("")
      match issue.run_id {
        Some(run_id) => {
          output.write_string(" · run ")
          output.write_string(html_escape(run_id))
        }
        None => ()
      }
      output.write_string(": ")
      output.write_string(html_escape(issue.message))
      output.write_string("
\n")
    }
    output.write_string("
\n")
  }
  output.write_string(
    "
\n",
  )
  output.to_string()
}