Merge pull request #2050 from effigies/feat/phenotype-datatype

[ENH] Define "phenotype" as a data type not nested inside subjects

Author: effigies

src/schema/objects/common_principles.yaml

@@ -13,7 +13,6 @@ data_type:
   description: |
     A functional group of different types of data.
     Data files are contained in a directory named for the data type.
-    In raw datasets, the data type directory is nested inside subject and (optionally) session directories.
     BIDS defines the following data types:
 
         1.  `func` (task based and resting state functional MRI)
@@ -44,6 +43,13 @@ data_type:
 
         14. `mrs` (magnetic resonance spectroscopy)
 
+        15. `phenotype` (measurement and survey data)
+
+    For files that are subject- and session- specific, the data type directory
+    is nested inside those directories.
+    `phenotype` data files are aggregated across subjects and sessions,
+    and so the `phenotype/` directory is placed in the dataset root.
+
 dataset:
   display_name: Dataset
   description: |

src/schema/objects/datatypes.yaml

@@ -61,6 +61,13 @@ pet:
   display_name: Positron Emission Tomography
   description: |
     Positron emission tomography data
+phenotype:
+  value: phenotype
+  display_name: Phenotype
+  description: |
+    Participant level measurement data
+    (for example, responses from multiple questionnaires)
+    split into individual files separate from `participants.tsv`.
 nirs:
   value: nirs
   display_name: Near-Infrared Spectroscopy

tools/schemacode/src/bidsschematools/__main__.py

@@ -149,9 +149,6 @@ def pre_receive_hook(schema, input_, output):
         )
 
     regexes = [rule["regex"] for rule in all_rules]
-    # XXX Hack for phenotype files - this can be removed once we
-    # have a schema definition for them
-    regexes.append(r"phenotype/.*\.(tsv|json)")
 
     output = sys.stdout if output == "-" else open(output, "w")
 

tools/schemacode/src/bidsschematools/data/tests/test_rules.py

@@ -101,11 +101,6 @@ def test_rule_objects(schema_obj):
 
                 # Build a list of items mentioned in rules, but not found in objects.
                 if use not in object_values:
-                    if (use, object_type) == ("phenotype", "datatypes"):
-                        # Special case: phenotype is a top-level directory
-                        # that acts like a datatype, but we don't want to
-                        # define it that way in the glossary, currently.
-                        continue
                     temp_path = path[:]
                     if is_list:
                         temp_path[-1] += f"[{i_use}]"