fix: correct CDISC codelists and remove SDTMIG 3.4 rules that reject conformant data

pointblank/metadata/_adam_templates.py

@@ -341,7 +341,7 @@ def _adsl_template() -> ADaMDatasetTemplate:
             ),
             ADaMVariableSpec(
                 "DCTREAS",
-                "Reason for Discontinuation from Treatment",
+                "Reason for Discontinuation of Treatment",
                 "Char",
                 core="Perm",
                 max_length=200,
@@ -475,7 +475,7 @@ def _bds_template() -> ADaMDatasetTemplate:
             ),
             ADaMVariableSpec(
                 "ANL01FL",
-                "Analysis Record Flag 01",
+                "Analysis Flag 01",
                 "Char",
                 core="Perm",
                 max_length=1,
@@ -490,9 +490,9 @@ def _bds_template() -> ADaMDatasetTemplate:
                 controlled_term="NY",
             ),
             # ── Traceability ──
-            ADaMVariableSpec("SRCDOM", "Source Data Domain", "Char", core="Perm", max_length=8),
-            ADaMVariableSpec("SRCVAR", "Source Data Variable", "Char", core="Perm", max_length=40),
-            ADaMVariableSpec("SRCSEQ", "Source Data Sequence Number", "Num", core="Perm"),
+            ADaMVariableSpec("SRCDOM", "Source Data", "Char", core="Perm", max_length=8),
+            ADaMVariableSpec("SRCVAR", "Source Variable", "Char", core="Perm", max_length=40),
+            ADaMVariableSpec("SRCSEQ", "Source Sequence Number", "Num", core="Perm"),
             # ── Criterion Variables ──
             ADaMVariableSpec("CRIT1", "Analysis Criterion 1", "Char", core="Perm", max_length=200),
             ADaMVariableSpec(
@@ -639,12 +639,14 @@ def _adae_template() -> ADaMDatasetTemplate:
             ADaMVariableSpec("AENDTM", "Analysis End Datetime", "Num", core="Perm"),
             ADaMVariableSpec("ASTDY", "Analysis Start Relative Day", "Num", core="Perm"),
             ADaMVariableSpec("AENDY", "Analysis End Relative Day", "Num", core="Perm"),
-            ADaMVariableSpec("ADURN", "AE Duration (N)", "Num", core="Perm"),
-            ADaMVariableSpec("ADURU", "AE Duration Units", "Char", core="Perm", max_length=40),
+            ADaMVariableSpec("ADURN", "Analysis Duration (N)", "Num", core="Perm"),
+            ADaMVariableSpec(
+                "ADURU", "Analysis Duration Units", "Char", core="Perm", max_length=40
+            ),
             # ── Flags ──
             ADaMVariableSpec(
                 "TRTEMFL",
-                "Treatment Emergent Flag",
+                "Treatment Emergent Analysis Flag",
                 "Char",
                 core="Cond",
                 max_length=1,
@@ -721,13 +723,13 @@ def _adtte_template() -> ADaMDatasetTemplate:
             # ── Time-to-Event Variables ──
             ADaMVariableSpec("AVAL", "Analysis Value", "Num", required=True, core="Req"),
             ADaMVariableSpec(
-                "STARTDT", "Time-to-Event Origin Date", "Num", required=True, core="Req"
+                "STARTDT", "Time-to-Event Origin Date for Subject", "Num", required=True, core="Req"
             ),
             ADaMVariableSpec("ADT", "Analysis Date", "Num", required=True, core="Req"),
             ADaMVariableSpec("CNSR", "Censor", "Num", required=True, core="Req"),
             ADaMVariableSpec(
                 "EVNTDESC",
-                "Event Description",
+                "Event or Censoring Description",
                 "Char",
                 core="Cond",
                 max_length=200,
@@ -742,9 +744,9 @@ def _adtte_template() -> ADaMDatasetTemplate:
                 condition="Required for traceability",
             ),
             # ── Supporting Variables ──
-            ADaMVariableSpec("SRCDOM", "Source Data Domain", "Char", core="Perm", max_length=8),
-            ADaMVariableSpec("SRCVAR", "Source Data Variable", "Char", core="Perm", max_length=40),
-            ADaMVariableSpec("SRCSEQ", "Source Data Sequence Number", "Num", core="Perm"),
+            ADaMVariableSpec("SRCDOM", "Source Data", "Char", core="Perm", max_length=8),
+            ADaMVariableSpec("SRCVAR", "Source Variable", "Char", core="Perm", max_length=40),
+            ADaMVariableSpec("SRCSEQ", "Source Sequence Number", "Num", core="Perm"),
         ],
     )
 

pointblank/metadata/_sdtm_templates.py

@@ -617,15 +617,15 @@ def _lb_template() -> SDTMDomainTemplate:
             ),
             SDTMVariableSpec(
                 "LBORNRLO",
-                "Reference Range Lower Limit-Orig Unit",
+                "Reference Range Lower Limit in Orig Unit",
                 "Char",
                 "Qualifier",
                 max_length=40,
                 core="Exp",
             ),
             SDTMVariableSpec(
                 "LBORNRHI",
-                "Reference Range Upper Limit-Orig Unit",
+                "Reference Range Upper Limit in Orig Unit",
                 "Char",
                 "Qualifier",
                 max_length=40,
@@ -1058,7 +1058,9 @@ def _ds_template() -> SDTMDomainTemplate:
                 max_length=64,
                 core="Exp",
             ),
-            SDTMVariableSpec("DSSTDY", "Study Day of Start of Event", "Num", "Timing", core="Perm"),
+            SDTMVariableSpec(
+                "DSSTDY", "Study Day of Start of Disposition Event", "Num", "Timing", core="Perm"
+            ),
         ],
     )
 
@@ -1154,15 +1156,15 @@ def _mh_template() -> SDTMDomainTemplate:
             ),
             SDTMVariableSpec(
                 "MHSTDTC",
-                "Start Date/Time of Medical History",
+                "Start Date/Time of Medical History Event",
                 "Char",
                 "Timing",
                 max_length=64,
                 core="Perm",
             ),
             SDTMVariableSpec(
                 "MHENDTC",
-                "End Date/Time of Medical History",
+                "End Date/Time of Medical History Event",
                 "Char",
                 "Timing",
                 max_length=64,

tests/test_metadata_template_labels.py

@@ -0,0 +1,62 @@
+"""
+SDTM and ADaM templates must fit SAS transport (XPT v5) limits and use the IG wording.
+
+XPT v5, the format required for FDA submissions, caps variable names at 8 characters and
+variable and dataset labels at 40 characters.
+"""
+
+from __future__ import annotations
+
+import pytest
+
+from pointblank.metadata._adam_templates import get_adam_dataset, list_adam_datasets
+from pointblank.metadata._sdtm_templates import get_sdtm_domain, list_sdtm_domains
+
+TEMPLATES = [("SDTM", d, get_sdtm_domain(d)) for d in list_sdtm_domains()] + [
+    ("ADaM", d, get_adam_dataset(d)) for d in list_adam_datasets()
+]
+
+
+@pytest.mark.parametrize(
+    "template", [t for _, _, t in TEMPLATES], ids=[f"{s}-{d}" for s, d, _ in TEMPLATES]
+)
+def test_template_fits_sas_transport_limits(template):
+    name = getattr(template, "domain", None) or template.name
+    assert len(name) <= 8
+    assert len(template.label) <= 40, template.label
+
+    too_long = [
+        f"{v.name}: {v.label!r} ({len(v.label)})" for v in template.variables if len(v.label) > 40
+    ]
+    assert too_long == []
+    assert [v.name for v in template.variables if len(v.name) > 8] == []
+
+
+@pytest.mark.parametrize(
+    "get, dataset, variable, label",
+    [
+        # SDTMIG 3.4
+        (get_sdtm_domain, "DS", "DSSTDY", "Study Day of Start of Disposition Event"),
+        (get_sdtm_domain, "MH", "MHSTDTC", "Start Date/Time of Medical History Event"),
+        (get_sdtm_domain, "MH", "MHENDTC", "End Date/Time of Medical History Event"),
+        (get_sdtm_domain, "LB", "LBORNRLO", "Reference Range Lower Limit in Orig Unit"),
+        (get_sdtm_domain, "LB", "LBORNRHI", "Reference Range Upper Limit in Orig Unit"),
+        # ADaMIG 1.3
+        (get_adam_dataset, "ADSL", "DCTREAS", "Reason for Discontinuation of Treatment"),
+        (get_adam_dataset, "BDS", "ANL01FL", "Analysis Flag 01"),
+        (get_adam_dataset, "BDS", "SRCDOM", "Source Data"),
+        (get_adam_dataset, "BDS", "SRCVAR", "Source Variable"),
+        (get_adam_dataset, "BDS", "SRCSEQ", "Source Sequence Number"),
+        # ADaM OCCDS
+        (get_adam_dataset, "ADAE", "ADURN", "Analysis Duration (N)"),
+        (get_adam_dataset, "ADAE", "ADURU", "Analysis Duration Units"),
+        (get_adam_dataset, "ADAE", "TRTEMFL", "Treatment Emergent Analysis Flag"),
+        # ADaM BDS for time-to-event
+        (get_adam_dataset, "ADTTE", "STARTDT", "Time-to-Event Origin Date for Subject"),
+        (get_adam_dataset, "ADTTE", "EVNTDESC", "Event or Censoring Description"),
+        (get_adam_dataset, "ADTTE", "SRCDOM", "Source Data"),
+    ],
+)
+def test_template_labels_use_ig_wording(get, dataset, variable, label):
+    spec = next(v for v in get(dataset).variables if v.name == variable)
+    assert spec.label == label