Ongoing Conditions with Partial Dates

Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

Task: Would a real study need this derivation, specified this way? Does it follow CDISC SDTM: variable names, controlled terms, record structure? Flag any rule that is ambiguous or that a sponsor would handle differently.
Inputs: Do they look like data collected in a real trial, and do they include the situations you would expect to meet in one?
Expected output: Would independent QC programming reproduce every value from these inputs and rules?

The other tabs beside Comments are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: build the medical history (MH) records from the history form, keeping each condition's start at the precision it was recorded and showing whether it ended before, or was still going at, the screening visit.

Input: one record per condition reported on the form, each numbered by its record sequence (MHSEQ), with the collected start year and month, the collected end date, the ongoing tick box, and the screening visit date recorded on the same form.

Variables:

MHTERM is the condition as written on the form.
MHSTDTC is the start of the condition at the precision recorded: the year alone (for example 2015) when only the year was known, or year and month (for example 2019-03); empty when no year was recorded.
MHENDTC is the date the condition ended, when an end was recorded.
MHENRTPT says how the condition's end relates to the screening visit: ONGOING when the tick box said it was still active, BEFORE when the recorded end date comes before the screening visit date recorded on the form; empty otherwise (for example when the recorded end date is on or after the screening visit date).
MHENTPT names the visit the end reference is measured against, SCREENING; empty when there is no end reference.

Note: a condition still active at the screening visit carries no end date: the ongoing answer is the record of its end status, and the screening visit is named as the reference for both ONGOING and BEFORE.

YAML specification

1 spec file

spec.yaml

Edit96 lines

1schema_version: "1.0"2domain: MH3keys: [STUDYID, USUBJID, MHSEQ]4input:5  MH_FORM: input/mh_form.csv67output:8  path: mh.csv9  columns: [STUDYID, USUBJID, MHSEQ, MHTERM, MHSTDTC, MHENDTC, MHENRTPT,10            MHENTPT]11  order_by: [STUDYID, USUBJID, MHSEQ]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: MH_FORM.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: MH_FORM.USUBJID2324  - name: MHSEQ25    type: int26    label: Sequence Number27    derivation: MH_FORM.MHSEQ2829  - name: MHTERM30    type: str31    label: Reported Term for the Medical History Condition32    derivation: MH_FORM.MHTERM33    verifications:34      not_missing: {}3536  # The collected start year alone, or year and month joined with a hyphen.37  # A month with no year, or no year at all, leaves the start empty.38  - name: MHSTDTC39    type: str40    label: Start Date/Time of Medical History Condition41    derivation:42      case:43        - when: "MH_FORM.MHSTYY IS NOT NULL AND MH_FORM.MHSTMM IS NULL"44          then: MH_FORM.MHSTYY45        - when: "MH_FORM.MHSTYY IS NOT NULL AND MH_FORM.MHSTMM IS NOT NULL"46          then:47            str_template:48              template: "{MH_FORM.MHSTYY}-{MH_FORM.MHSTMM}"4950  - name: MHENDTC51    type: str52    label: End Date/Time of Medical History Condition53    derivation: MH_FORM.MHENDTC5455  # An ongoing answer of Y wins. Otherwise BEFORE when the end date is56  # earlier than the screening date (both compared as ISO 8601 text); an57  # end on or after screening, or a missing date, leaves it empty.58  - name: MHENRTPT59    type: str60    label: End Reference Relative to the Screening Visit61    derivation:62      case:63        - when: "MH_FORM.MHONGO = 'Y'"64          then: {literal: ONGOING}65        - when: "MHENDTC < MH_FORM.SCRFDTC"66          then: {literal: BEFORE}67    verifications:68      allowed_values:69        values: [ONGOING, BEFORE]7071  - name: MHENTPT72    type: str73    label: Reference Time Point Name74    derivation:75      case:76        - when: "MHENRTPT IS NOT NULL"77          then: {literal: SCREENING}7879verifications:80  - unique:81      columns: [STUDYID, USUBJID, MHSEQ]82  - row_count:83      min: 784      max: 785  - assert:86      id: ongoing-has-no-end-date87      when: "MHENRTPT = 'ONGOING'"88      require: "MHENDTC IS NULL"89  - assert:90      id: ended-before-has-end-date91      when: "MHENRTPT = 'BEFORE'"92      require: "MHENDTC IS NOT NULL"93  - assert:94      id: end-reference-names-screening95      when: "MHENRTPT IS NOT NULL"96      require: "MHENTPT = 'SCREENING'"

Inputs

Under review1 source file

input/mh_form.csv

Edit7 rows

input/mh_form.csv
STUDYID	MHSEQ	MHTERM	MHSTYY	MHSTMM	MHENDTC	MHONGO	SCRFDTC
YAMAA-01	1	HYPERTENSION	2015	—	—	Y	2021-06-01
YAMAA-01	2	HYPERLIPIDEMIA	2019	03	2020-11-30	N	2021-06-01
YAMAA-01	1	ASTHMA	2017	06	—	N	2022-05-10
YAMAA-01	2	ECZEMA	2020	—	2022-02-14	N	2022-05-10
YAMAA-01	1	MIGRAINE	2018	11	—	Y	2021-09-20
YAMAA-01	2	TYPE 2 DIABETES MELLITUS	—	—	—	N	2021-09-20
YAMAA-01	1	GOUT	2019	05	2021-07-15	N	2021-06-01

Expected output

Under review7 expected rows

expected/mh.csv

Edit7 rows

expected/mh.csv
STUDYID	MHSEQ	MHTERM	MHSTDTC	MHENDTC	MHENRTPT	MHENTPT
YAMAA-01	1	HYPERTENSION	2015	—	ONGOING	SCREENING
YAMAA-01	2	HYPERLIPIDEMIA	2019-03	2020-11-30	BEFORE	SCREENING
YAMAA-01	1	ASTHMA	2017-06	—	—	—
YAMAA-01	2	ECZEMA	2020	2022-02-14	BEFORE	SCREENING
YAMAA-01	1	MIGRAINE	2018-11	—	ONGOING	SCREENING
YAMAA-01	2	TYPE 2 DIABETES MELLITUS	—	—	—	—
YAMAA-01	1	GOUT	2019-05	2021-07-15	—	—

Shaded columns are derived— = missing value

Comments and assessment materials

Variable Name	Variable Label	Type	Controlled Terms or Format	Origin	Conversion Definition	Variable Type	Variable Order
STUDYID	Study Identifier	Char		Collected	Copy value from MH_FORM.STUDYID.	SDTM	1
USUBJID	Unique Subject Identifier	Char		Collected	Copy value from MH_FORM.USUBJID.	SDTM	2
MHSEQ	Sequence Number	Num		Collected	Copy value from MH_FORM.MHSEQ.	SDTM	3
MHTERM	Reported Term for the Medical History Condition	Char		Collected	Copy value from MH_FORM.MHTERM.	SDTM	4
MHSTDTC	Start Date/Time of Medical History Condition	Char		Derived	If MH_FORM.MHSTYY IS NOT NULL AND MH_FORM.MHSTMM IS NULL then "MH_FORM.MHSTYY"; If MH_FORM.MHSTYY IS NOT NULL AND MH_FORM.MHSTMM IS NOT NULL then fill the template "{MH_FORM.MHSTYY}-{MH_FORM.MHSTMM}"; otherwise blank.	SDTM	5
MHENDTC	End Date/Time of Medical History Condition	Char		Collected	Copy value from MH_FORM.MHENDTC.	SDTM	6
MHENRTPT	End Reference Relative to the Screening Visit	Char	ONGOING, BEFORE	Derived	If MH_FORM.MHONGO = 'Y' then "ONGOING"; If MHENDTC < MH_FORM.SCRFDTC then "BEFORE"; otherwise blank.	SDTM	7
MHENTPT	Reference Time Point Name	Char		Derived	If MHENRTPT IS NOT NULL then "SCREENING"; otherwise blank.	SDTM	8

Variable	Permitted values
MHENRTPT	ONGOING, BEFORE

Version	Date	Author	Description
1.3	2026-09-29	yamaa docs build	Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.2	2026-09-29	yamaa docs build	Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.1	2026-09-29	yamaa docs build	Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0		yamaa docs build	Initial generation from spec.yaml

prompts/sdtm-mh-ongoing-conditions/full.md

Edit22 lines

Following CDISC SDTM standards, use the provided MH_FORM dataset to create an MH dataset with one record per reported condition.

The output dataset should contain the following columns in this order: STUDYID, USUBJID, MHSEQ, MHTERM, MHSTDTC, MHENDTC, MHENRTPT, MHENTPT

MHTERM is the condition as written on the form. MHSTDTC is the start of the condition at the precision recorded: the year alone when only the year was known, or year and month; it has no value when no year was recorded. MHENDTC is the date the condition ended, when an end was recorded; a condition still active at the screening visit carries no end date.

MHENRTPT says how the condition's end relates to the screening visit: ONGOING when the tick box said it was still active, BEFORE when the recorded end date comes before the screening visit date recorded on the form, and no value otherwise (for example when the recorded end date is on or after the screening visit date). MHENTPT names the visit the end reference is measured against, SCREENING; it has no value when there is no end reference.

Read the source datasets from /app/input and save the completed dataset as /app/output/mh.csv.

prompts/sdtm-mh-ongoing-conditions/conventions.md

Edit11 lines

Following CDISC SDTM standards, use the provided MH_FORM dataset to create an MH dataset with one record per reported condition.

The output dataset should contain the following columns in this order: STUDYID, USUBJID, MHSEQ, MHTERM, MHSTDTC, MHENDTC, MHENRTPT, MHENTPT

MHENRTPT is ONGOING, BEFORE, or has no value. MHENTPT is SCREENING or has no value.

Read the source datasets from /app/input and save the completed dataset as /app/output/mh.csv.

prompts/sdtm-mh-ongoing-conditions/brief.md

Edit8 lines

Following CDISC SDTM standards, use the provided MH_FORM dataset to create an MH dataset with one record per reported condition.

The output dataset should contain the following columns in this order: STUDYID, USUBJID, MHSEQ, MHTERM, MHSTDTC, MHENDTC, MHENRTPT, MHENTPT

Read the source datasets from /app/input and save the completed dataset as /app/output/mh.csv.

run.R

Edit4 lines

1library(yamaa)23mh <- yamaa_domain("spec.yaml")$output4mh

run.py

Edit4 lines

1import yamaa23mh = yamaa.yamaa_domain("spec.yaml").output4mh

solutions/sdtm-mh-ongoing-conditions/result.R

Edit40 lines

1# Reference solution for the yamaa benchmark sdtm-mh-ongoing-conditions (R track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67library(dplyr, warn.conflicts = FALSE)8library(readr)910mh_form <- read_csv(11  "/app/input/mh_form.csv",12  col_types = cols(MHSEQ = col_integer(), .default = col_character())13)1415mh <- mh_form |>16  mutate(17    MHSTDTC = case_when(18      is.na(MHSTYY) | MHSTYY == "" ~ NA_character_,19      is.na(MHSTMM) | MHSTMM == "" ~ MHSTYY,20      TRUE ~ paste0(MHSTYY, "-", sprintf("%02d", as.integer(MHSTMM)))21    ),22    # A condition still active at screening carries no end date.23    MHENDTC = if_else(MHONGO == "Y" | is.na(MHENDTC) | MHENDTC == "",24      NA_character_, MHENDTC25    ),26    MHENRTPT = case_when(27      MHONGO == "Y" ~ "ONGOING",28      !is.na(MHENDTC) & MHENDTC != "" &29        !is.na(SCRFDTC) & MHENDTC < SCRFDTC ~ "BEFORE",30      TRUE ~ NA_character_31    ),32    MHENTPT = if_else(is.na(MHENRTPT), NA_character_, "SCREENING")33  ) |>34  arrange(USUBJID, MHSEQ) |>35  select(36    STUDYID, USUBJID, MHSEQ, MHTERM, MHSTDTC, MHENDTC, MHENRTPT, MHENTPT37  )3839dir.create("/app/output", showWarnings = FALSE)40write_csv(mh, "/app/output/mh.csv", na = "")

solutions/sdtm-mh-ongoing-conditions/result.py

Edit81 lines

1# Reference solution for the yamaa benchmark sdtm-mh-ongoing-conditions (Python track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67from pathlib import Path89import polars as pl101112def _present(value) -> bool:13    return value is not None and str(value) != ""141516mh_form = pl.read_csv("/app/input/mh_form.csv", infer_schema=False)1718rows = []19for row in mh_form.to_dicts():20    year, month = row.get("MHSTYY"), row.get("MHSTMM")21    if not _present(year):22        mhstdtc = None23    elif not _present(month):24        mhstdtc = str(year)25    else:26        mhstdtc = f"{year}-{str(month).zfill(2)}"2728    # A condition still active at screening carries no end date.29    ongoing = str(row.get("MHONGO") or "") == "Y"30    endtc = row.get("MHENDTC")31    if ongoing or not _present(endtc):32        mhendtc = None33    else:34        mhendtc = str(endtc)3536    scrfdtc = str(row.get("SCRFDTC") or "")37    if ongoing:38        mhenrtpt = "ONGOING"39    elif _present(endtc) and _present(scrfdtc) and str(endtc) < scrfdtc:40        mhenrtpt = "BEFORE"41    else:42        mhenrtpt = None43    mhentpt = "SCREENING" if mhenrtpt is not None else None4445    rows.append(46        {47            "STUDYID": row["STUDYID"],48            "USUBJID": row["USUBJID"],49            "MHSEQ": row["MHSEQ"],50            "MHTERM": row["MHTERM"],51            "MHSTDTC": mhstdtc,52            "MHENDTC": mhendtc,53            "MHENRTPT": mhenrtpt,54            "MHENTPT": mhentpt,55        }56    )5758mh = (59    pl.DataFrame(60        rows,61        schema={62            "STUDYID": pl.String,63            "USUBJID": pl.String,64            "MHSEQ": pl.String,65            "MHTERM": pl.String,66            "MHSTDTC": pl.String,67            "MHENDTC": pl.String,68            "MHENRTPT": pl.String,69            "MHENTPT": pl.String,70        },71    )72    .with_columns(pl.col("MHSEQ").cast(pl.Int64).alias("_seq"))73    .sort(["USUBJID", "_seq"])74    .select(75        "STUDYID", "USUBJID", "MHSEQ", "MHTERM", "MHSTDTC", "MHENDTC",76        "MHENRTPT", "MHENTPT",77    )78)7980Path("/app/output").mkdir(exist_ok=True)81mh.write_csv("/app/output/mh.csv")

solutions/sdtm-mh-ongoing-conditions/result.sas

Edit18 lines

1/* opensas reference solution for the yamaa benchmark sdtm-mh-ongoing-conditions.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data mh_form;6  length STUDYID USUBJID MHTERM MHSTYY MHSTMM MHENDTC MHONGO SCRFDTC $1024;7  infile "/app/input/mh_form.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. MHSEQ MHTERM : $char1024. MHSTYY : $char1024. MHSTMM : $char1024. MHENDTC : $char1024. MHONGO : $char1024. SCRFDTC : $char1024.;9run;1011data result; set mh_form; length DOMAIN $2 MHSTDTC MHENRTPT MHENTPT $1024; DOMAIN='MH'; MHSTDTC=''; MHENRTPT=''; MHENTPT='';12if not missing(MHSTYY) then do; MHSTDTC=MHSTYY; if not missing(MHSTMM) then MHSTDTC=catx('-',MHSTYY,MHSTMM); end;13if MHONGO='Y' then do; MHENDTC=''; MHENRTPT='ONGOING'; end; else if not missing(MHENDTC) and not missing(SCRFDTC) and MHENDTC<SCRFDTC then MHENRTPT='BEFORE';14if not missing(MHENRTPT) then MHENTPT='SCREENING'; run;15proc sql;16  create table final as select STUDYID, USUBJID, MHSEQ, MHTERM, MHSTDTC, MHENDTC, MHENRTPT, MHENTPT from result;17quit;18proc export data=final outfile="/app/output/mh.csv" dbms=csv replace; run;

input/mh_form.csv

expected/mh.csv

Comments

Mapping spec

Agent prompt

prompts/sdtm-mh-ongoing-conditions/full.md

prompts/sdtm-mh-ongoing-conditions/conventions.md

prompts/sdtm-mh-ongoing-conditions/brief.md

yamaa code

run.R

run.py

Solution without yamaa

solutions/sdtm-mh-ongoing-conditions/result.R

solutions/sdtm-mh-ongoing-conditions/result.py

solutions/sdtm-mh-ongoing-conditions/result.sas