Add returnUnmatched to spec options

adtl/__init__.py

@@ -20,8 +20,10 @@
 import requests
 import fastjsonschema
 from tqdm import tqdm
+import warnings
 
 import adtl.transformations as tf
+from adtl.transformations import AdtlTransformationWarning
 
 SUPPORTED_FORMATS = {"json": json.load, "toml": tomli.load}
 DEFAULT_DATE_FORMAT = "%Y-%m-%d"
@@ -77,6 +79,7 @@ def get_value_unhashed(row: StrDict, rule: Rule, ctx: Context = None) -> Any:
         if "apply" in rule:
             # apply data transformations.
             transformation = rule["apply"]["function"]
+            params = None
             if "params" in rule["apply"]:
                 params = []
                 for i in range(len(rule["apply"]["params"])):
@@ -100,21 +103,25 @@ def get_value_unhashed(row: StrDict, rule: Rule, ctx: Context = None) -> Any:
                     else:
                         params.append(rule["apply"]["params"][i])
 
-                try:
-                    value = getattr(tf, transformation)(value, *params)
-                except AttributeError:
-                    raise AttributeError(
-                        f"Error using a data transformation: Function {transformation} "
-                        "has not been defined."
-                    )
-            else:
-                try:
-                    value = getattr(tf, transformation)(value)
-                except AttributeError:
-                    raise AttributeError(
-                        f"Error using a data transformation: Function {transformation} "
-                        "has not been defined."
-                    )
+            try:
+                with warnings.catch_warnings():
+                    warnings.simplefilter("error", category=AdtlTransformationWarning)
+                    if params:
+                        value = getattr(tf, transformation)(value, *params)
+                    else:
+                        value = getattr(tf, transformation)(value)
+            except AttributeError:
+                raise AttributeError(
+                    f"Error using a data transformation: Function {transformation} "
+                    "has not been defined."
+                )
+            except AdtlTransformationWarning as e:
+                if ctx and ctx.get("returnUnmatched"):
+                    warnings.warn(str(e), AdtlTransformationWarning)
+                    return value
+                else:
+                    logging.error(str(e))
+                    return None
             return value
         if value == "":
             return None
@@ -123,10 +130,14 @@ def get_value_unhashed(row: StrDict, rule: Rule, ctx: Context = None) -> Any:
                 value = value.lower()
                 rule["values"] = {k.lower(): v for k, v in rule["values"].items()}
 
-            if rule.get("ignoreMissingKey"):
+            if rule.get("ignoreMissingKey") or (ctx and ctx.get("returnUnmatched")):
                 value = rule["values"].get(value, value)
             else:
                 value = rule["values"].get(value)
+
+            # recheck if value is empty after mapping (use to map values to None)
+            if value == "":
+                return None
         # Either source_unit / unit OR source_date / date triggers conversion
         # do not parse units if value is empty
         if "source_unit" in rule and "unit" in rule:
@@ -142,6 +153,9 @@ def get_value_unhashed(row: StrDict, rule: Rule, ctx: Context = None) -> Any:
             try:
                 value = pint.Quantity(float(value), source_unit).to(unit).m
             except ValueError:
+                if ctx and ctx.get("returnUnmatched"):
+                    logging.debug(f"Could not convert {value} to a floating point")
+                    return value
                 raise ValueError(f"Could not convert {value} to a floating point")
         if "source_date" in rule or (ctx and ctx.get("is_date")):
             assert "source_unit" not in rule and "unit" not in rule
@@ -156,6 +170,8 @@ def get_value_unhashed(row: StrDict, rule: Rule, ctx: Context = None) -> Any:
                     value = datetime.strptime(value, source_date).strftime(target_date)
                 except (TypeError, ValueError):
                     logging.info(f"Could not parse date: {value}")
+                    if ctx and ctx.get("returnUnmatched"):
+                        return value
                     return None
         return value
     elif "combinedType" in rule:
@@ -609,6 +625,7 @@ def ctx(self, attribute: str):
                 if self.header.get("skipFieldPattern")
                 else False
             ),
+            "returnUnmatched": self.header.get("returnUnmatched", False),
         }
 
     def validate_spec(self):
@@ -1042,6 +1059,10 @@ def main(argv=None):
     include_defs = args.include_def or []
     spec = Parser(args.spec, include_defs=include_defs, quiet=args.quiet)
 
+    # check for incompatible options
+    if spec.header.get("returnUnmatched") and args.parquet:
+        raise ValueError("returnUnmatched and parquet options are incompatible")
+
     # run adtl
     adtl_output = spec.parse(args.file, encoding=args.encoding)
     adtl_output.save(args.output or spec.name, args.parquet)

adtl/transformations.py

@@ -1,6 +1,5 @@
 """ Functions which can be applied to source fields, allowing extensibility """
 
-import logging
 from typing import Any, Optional, List
 from datetime import datetime, timedelta, date
 
@@ -17,6 +16,12 @@
 
 from typing import Literal, Union
 
+import warnings
+
+
+class AdtlTransformationWarning(UserWarning):
+    pass
+
 
 def isNotNull(value: Optional[str]) -> bool:
     "Returns whether value is not null or an empty string"
@@ -55,6 +60,12 @@ def wordSubstituteSet(value: str, *params) -> List[str]:
         for match, subst in sub_map.items():
             if re.search(r"\b" + match + r"\b", value, re.IGNORECASE):
                 out.append(subst)
+    if not out and (value not in [None, ""]):
+        warnings.warn(
+            f"No matches found for: '{value}'",
+            AdtlTransformationWarning,
+            stacklevel=2,
+        )
     return sorted(set(out)) if out else None
 
 
@@ -118,18 +129,19 @@ def yearsElapsed(
     bd_format: str = "%Y-%m-%d",
     cd_format: str = "%Y-%m-%d",
 ):
-    """Returns the number of years elapsed between two dates, useful for calculating ages
+    """
+    Returns the number of years elapsed between two dates, useful for calculating ages
 
     Args:
         birthdate: Start date of duration
         currentdate: End date of duration
         epoch: Epoch year after which dates will be converted to the last century.
             As an example, if epoch is 2022, then the date 1/1/23 will be converted
             to the January 1, 1923.
-        bd_format: Date format for *birthdate* specified using :manpage:`strftime(3)` conventions.
-            Defaults to ISO format ("%Y-%m-%d")
-        cd_format: Date format for *currentdate* specified using :manpage:`strftime(3)` conventions.
-            Defaults to ISO format ("%Y-%m-%d")
+        bd_format: Date format for *birthdate* specified using :manpage:`strftime(3)`
+            conventions. Defaults to ISO format ("%Y-%m-%d")
+        cd_format: Date format for *currentdate* specified using :manpage:`strftime(3)`
+            conventions. Defaults to ISO format ("%Y-%m-%d")
 
     Returns:
         int | None: Number of years elapsed or None if invalid dates were encountered
@@ -145,8 +157,15 @@ def yearsElapsed(
 
     cd = datetime.strptime(currentdate, cd_format)
 
-    days = cd - bd
-    return pint.Quantity(days.days, "days").to("years").m
+    try:
+        days = cd - bd
+        return pint.Quantity(days.days, "days").to("years").m
+    except ValueError:
+        warnings.warn(
+            f"Failed calculation yearsElapsed: {birthdate}, {currentdate}",
+            AdtlTransformationWarning,
+            stacklevel=2,
+        )
 
 
 def durationDays(startdate: str, currentdate: str) -> int:
@@ -210,15 +229,19 @@ def makeDate(year: str, month: str, day: str) -> str:
     try:
         year, month, day = int(year), int(month), int(day)
     except ValueError:
-        logging.error(
-            f"Error in casting to integer: year={year}, month={month}, day={day}"
+        warnings.warn(
+            f"Could not construct date from: year={year}, month={month}, day={day}",
+            AdtlTransformationWarning,
+            stacklevel=2,
         )
         return None
     try:
         return date(year, month, day).isoformat()
     except ValueError:
-        logging.error(
-            f"Could not construct date from: year={year}, month={month}, day={day}"
+        warnings.warn(
+            f"Could not construct date from: year={year}, month={month}, day={day}",
+            AdtlTransformationWarning,
+            stacklevel=2,
         )
         return None
 
@@ -245,8 +268,10 @@ def makeDateTimeFromSeconds(
             tzinfo=zoneinfo.ZoneInfo(timezone)
         )
     except ValueError:
-        logging.error(
-            f"Could not convert date {date!r} from date format {date_format!r}"
+        warnings.warn(
+            f"Could not convert date {date!r} from date format {date_format!r}",
+            AdtlTransformationWarning,
+            stacklevel=2,
         )
         return None
     if time_seconds == "":
@@ -279,8 +304,10 @@ def makeDateTime(
             tzinfo=zoneinfo.ZoneInfo(timezone)
         )
     except ValueError:
-        logging.error(
-            f"Could not convert date {date!r} from date format {date_format!r}"
+        warnings.warn(
+            f"Could not convert date {date!r} from date format {date_format!r}",
+            AdtlTransformationWarning,
+            stacklevel=2,
         )
         return None
 
@@ -315,6 +342,11 @@ def splitDate(
     elif option == "day":
         return sd.day
     else:
+        warnings.warn(
+            f"Invalid option {option!r} for splitDate",
+            AdtlTransformationWarning,
+            stacklevel=2,
+        )
         return None
 
 
@@ -330,7 +362,8 @@ def startYear(
     Use to calculate year e.g. of birth from date (e.g. current date) and
     duration (e.g. age)
 
-    The date can be provided as a list of possible dates (if a hierarchy needs searching through)
+    The date can be provided as a list of possible dates (if a hierarchy needs
+    searching through)
 
     Args:
         duration: Duration value
@@ -442,7 +475,11 @@ def correctOldDate(date: str, epoch: float, format: str, return_datetime: bool =
     try:
         cd = datetime.strptime(date, format)
     except ValueError:
-        logging.error(f"Could not convert date {date!r} from date format {format!r}")
+        warnings.warn(
+            f"Could not convert date {date!r} from date format {format!r}",
+            AdtlTransformationWarning,
+            stacklevel=2,
+        )
         return None
 
     if cd.year >= epoch and "y" in format:

docs/specification.md

@@ -53,6 +53,13 @@ if not present in a datafile, following the same syntax as `fieldPattern` key.
 * **defaultDateFormat**: Default source date format, applied to all fields
   with either "date_" / "_date" in the field name or that have format date
   set in the JSON schema
+* **returnUnmatched**: Returns all values that are not able to be converted
+  according to the provided rules and formats. For fields with [value mappings](#field-with-value-mapping), it is equivalent to using `ignoreMissingKeys`. Fields using [data transformation functions](#data-transformations-(apply)) will issue a warning to the
+  terminal describing the error in the transformation. Transformations requiring multiple
+  parameters will only return the current field value that was not transformed.
+  > :warning: This is likely to return columns with non-matching datatypes. External json
+  validation may fail. This option is incompatible with the `--parquet` option to save
+  outputs as parquet files (which required a consistent type down each column).
 
 ## Validation
 

tests/__snapshots__/test_parser.ambr

@@ -47,6 +47,13 @@
 
   '''
 # ---
+# name: test_return_unmapped
+  '''
+  age,date_death,date_of_birth,diabetes_type,has_smoking,pregnancy_birth_weight_kg,subject_id
+  fifteen,2023,2023-11-20,no diabetes,today,eight,1
+
+  '''
+# ---
 # name: test_show_report
   '''
 

tests/parsers/return-unmapped.toml

@@ -0,0 +1,46 @@
+[adtl]
+  name = "test-return-unmapped"
+  description = "Example using returnUnmatched to return unmapped fields"
+  returnUnmatched = true
+
+[adtl.tables.subject]
+  kind = "groupBy"
+  groupBy = "subject_id"
+  aggregation = "lastNotNull"
+
+[subject]
+
+  [subject.subject_id]
+    field = "subjid"
+    description = "Subject ID"
+
+  [subject.date_of_birth]
+    field = "first_admit"
+    source_date = "%m"
+
+  [subject.age]
+    field = "age"
+    apply = {function = "getFloat"}
+
+  [subject.pregnancy_birth_weight_kg]
+    field = "weight"
+    unit = "kg"
+    source_unit = "lbs"
+
+  [subject.has_smoking]
+    field = "smoking"
+    values = { 1 = "current", 2 = "never", 3 = "former" }
+
+  [subject.diabetes_type]
+    field = "diabetes_type"
+
+    apply.function = "wordSubstituteSet"
+    apply.params = [
+      ["type[\\s\\-]?1", "type-1"],
+      ["type[\\s\\-]?2", "type-2"]
+      ]
+
+  [subject.date_death]
+    field = "death_year"
+    apply.function = "makeDate"
+    apply.params = ["$death_month", "$death_day"]

tests/sources/return-unmapped.csv

@@ -0,0 +1,2 @@
+subjid,redcap,first_admit,age,weight,smoking,diabetes_type,death_year,death_month,death_day
+1,admit,2023-11-20,fifteen,eight,today,no diabetes,2023,11,80

tests/test_parser.py

@@ -1227,6 +1227,22 @@ def test_main_parquet():
     Path("output-table.parquet").unlink()
 
 
+def test_main_parquet_error():
+    ARG = [
+        str(TEST_PARSERS_PATH / "return-unmapped.toml"),
+        str(TEST_SOURCES_PATH / "return-unmapped.csv"),
+        "-o",
+        "output",
+        "--encoding",
+        "utf-8",
+    ]
+
+    with pytest.raises(
+        ValueError, match="returnUnmatched and parquet options are incompatible"
+    ):
+        parser.main(ARG + ["--parquet"])
+
+
 @responses.activate
 def test_main_web_schema(snapshot):
     # test with schema on the web
@@ -1360,3 +1376,12 @@ def test_no_overwriting():
         .read_table("visit")
     )
     assert overwriting_output == OVERWRITE_OUTPUT
+
+
+def test_return_unmapped(snapshot):
+    transformed_csv_data = (
+        parser.Parser(TEST_PARSERS_PATH / "return-unmapped.toml")
+        .parse(TEST_SOURCES_PATH / "return-unmapped.csv")
+        .write_csv("subject")
+    )
+    assert transformed_csv_data == snapshot