[SCHEMA] Add patterns for format validation

src/schema/objects/formats.yaml

@@ -0,0 +1,115 @@
+---
+# This file defines valid patterns for different formats
+# Entity patterns
+label:
+  name: Label
+  description: |
+    Freeform labels without special characters.
+  pattern: '[0-9a-zA-Z]+'
+index:
+  name: Index
+  description: |
+    Non-negative, non-zero integers, optionally prefixed with leading zeros for sortability.
+    An index may not be all zeros.
+  pattern: '[0-9]*[1-9]+[0-9]*'
+# Metadata types
+string:
+  name: String
+  description: |
+    The basic string type (not a specific format).
+    This should allow any free-form string.
+  pattern: '.*'
+integer:
+  name: Integer
+  description: |
+    An integer which may be positive or negative.
+  pattern: '[+-]?\d+'
+number:
+  name: Number
+  description: |
+    A number which may be an integer or float, positive or negative.
+  pattern: '[+-]?([0-9]+([.][0-9]*)?|[.][0-9]+)([eE][+-]?[0-9]+)?'
+boolean:
+  name: Boolean
+  description: |
+    A boolean.
+    Must be either "true" or "false".
+  pattern: '(true|false)'
+# String formats
+date:
+  name: Date
+  description: |
+    A date in the form `"YYYY-MM-DD[Z]"`,
+    where [Z] is an optional, valid timezone code.
+  pattern: '[0-9]{4}-[0-9]{2}-[0-9]{2}([A-Z]{2,4})?'
+datetime:
+  name: Datetime
+  description: |
+    A datetime in the form `"YYYY-MM-DDThh:mm:ss[.000000][Z]"`,
+    where [.000000] is an optional subsecond resolution between 1 and 6 decimal points,
+    and [Z] is an optional, valid timezone code.
+  pattern: '[0-9]{4}-[0-9]{2}-[0-9]{2}T(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9](\.[0-9]{1,6})?([A-Z]{2,4})?'
+time:
+  name: Time
+  description: |
+    A time in the form `"hh:mm:ss"`.
+  pattern: '(?:2[0-3]|[01]?[0-9]):[0-5][0-9]:[0-5][0-9]'
+unit:
+  name: A standardized unit
+  description: |
+    A unit.
+    SI units in CMIXF formatting are RECOMMENDED
+    (see [Units](/02-common-principles.html#units)).
+
+    Currently this matches any string.
+
+    TODO: Somehow reference the actual unit options in the Units appendix.
+  pattern: '.*'
+stimuli_relative:
+  name: Path relative to the stimuli folder
+  description: |
+    A path to a stimulus file, relative to a `/stimuli` folder somewhere.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid path,
+    without starting with "/" (an absolute path) or "stimuli/"
+    (a relative path starting with the stimuli folder, rather than relative to that folder).
+  pattern: '(?!/)(?!stimuli/)[0-9a-zA-Z/\_\-\.]+'
+dataset_relative:
+  name: Path relative to the BIDS dataset folder
+  description: |
+    A path to a file, relative to the dataset folder.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid path,
+    without starting with "/" (an absolute path).
+  pattern: '(?!/)[0-9a-zA-Z/\_\-\.]+'
+participant_relative:
+  name: Path relative to the participant folder
+  description: |
+    A path to a file, relative to the participant's folder in the dataset.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid path,
+    without starting with "/" (an absolute path) or "sub/"
+    (a relative path starting with the participant folder, rather than relative to that folder).
+  pattern: '(?!/)(?!sub-)[0-9a-zA-Z/\_\-\.]+'
+rrid:
+  name: Research resource identifier
+  description: |
+    A [research resource identifier](https://scicrunch.org/resources).
+  pattern: 'RRID:.+_.+'
+uri:
+  name: Uniform resource indicator
+  description: |
+    A uniform resource indicator.
+  pattern: '(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?'
+bids_uri:
+  name: BIDS uniform resource indicator
+  description: |
+    A BIDS uniform resource indicator.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid URI,
+    starting with "bids:".
+  pattern: 'bids:[0-9a-zA-Z/#:\?\_\-\.]+'

src/schema/objects/metadata.yaml

@@ -1684,7 +1684,7 @@ MolarActivityMeasTime:
     Time to which molar radioactivity measurement above applies in the default
     unit `"hh:mm:ss"`.
   type: string
-  pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+  format: time
 MolarActivityUnits:
   name: MolarActivityUnits
   description: |
@@ -2447,7 +2447,7 @@ SoftwareRRID:
     Examples: The RRID for Psychtoolbox is 'SCR_002881',
     and that of PsychoPy is 'SCR_006571'.
   type: string
-  pattern: .+_.+
+  format: rrid
 SoftwareVersion:
   name: SoftwareVersion
   description: |
@@ -2535,7 +2535,7 @@ SpecificRadioactivityMeasTime:
     Time to which specific radioactivity measurement above applies in the default
     unit `"hh:mm:ss"`.
   type: string
-  pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+  format: time
 SpecificRadioactivityUnits:
   name: SpecificRadioactivityUnits
   description: |
@@ -2654,7 +2654,7 @@ TimeZero:
     in the unit "hh:mm:ss".
     This should be equal to `InjectionStart` or `ScanStart`.
   type: string
-  pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+  format: time
 TissueDeformationScaling:
   name: TissueDeformationScaling
   description: |

tools/schemacode/schemacode/tests/test_schema.py

@@ -27,3 +27,109 @@ def test_object_definitions(schema_obj):
 
             assert "name" in obj_def.keys(), obj_key
             assert "description" in obj_def.keys(), obj_key
+
+
+def test_formats(schema_obj):
+    """Test valid string patterns allowed by the specification."""
+    import re
+
+    # Check that valid strings match the search pattern.
+    GOOD_PATTERNS = {
+        "label": ["01", "test", "test01", "Test01"],
+        "index": ["01", "1", "10000", "00001"],
+        "string": ["any string is valid."],
+        "integer": ["5", "10", "-5", "-10"],
+        "number": [
+            "5",  # integers are allowed
+            "3.14",  # floats too
+            "-5",  # they can be negative
+            "-3.14",
+            "1e3",  # scientific notation is allowed
+            "-2.1E+5",
+        ],
+        "boolean": ["true", "false"],
+        "date": ["2022-01-05", "2022-01-05UTC", "2022-50-50"],
+        "datetime": [
+            "2022-01-05T13:16:30",
+            "2022-01-05T13:16:30.5",  # subsecond resolution is allowed
+            "2022-01-05T13:16:30.000005",  # up to 6 decimal points
+            "2022-01-05T13:16:30UTC",  # timezones are allowed
+            "2022-01-05T13:16:30.05UTC",
+        ],
+        "time": [
+            "13:16:30",
+            "09:00:00",
+            "9:00:00",  # leading zeros are not required for hours
+        ],
+        "unit": ["any string is valid."],
+        "stimuli_relative": ["any/arbitrary/path/file.txt"],
+        "dataset_relative": ["any/arbitrary/path/file.txt"],
+        "participant_relative": ["any/arbitrary/path/file.txt"],
+        "rrid": ["RRID:SCR_017398"],
+        "uri": ["foo://example.com:8042/over/there?name=ferret#nose"],
+        "bids_uri": [
+            "bids::sub-01/fmap/sub-01_dir-AP_epi.nii.gz",
+            "bids:ds000001:sub-02/anat/sub-02_T1w.nii.gz",
+            "bids:myderivatives:sub-03/func/sub-03_task-rest_space-MNI152_bold.nii.gz",
+        ],
+    }
+    for pattern, test_list in GOOD_PATTERNS.items():
+        pattern_format = schema_obj["objects"]["formats"][pattern]["pattern"]
+        search_pattern = "^" + pattern_format + "$"
+        search = re.compile(search_pattern)
+        for test_string in test_list:
+            assert bool(
+                search.fullmatch(test_string)
+            ), f"'{test_string}' is not a valid match for the pattern '{search.pattern}'"
+
+    # Check that invalid strings do not match the search pattern.
+    BAD_PATTERNS = {
+        "label": ["test_01", "!", "010101-", "01-01", "-01"],
+        "index": ["test", "0.1", "0-1", "0_1"],
+        "string": [],
+        "integer": ["3.14", "-3.14", "1.", "-1.", "string", "s1", "1%", "one"],
+        "number": ["string", "1%"],
+        "boolean": ["True", "False", "T", "F"],
+        "date": [
+            "05-01-2022",  # MM-DD-YYYY or DD-MM-YYYY
+            "05/01/2022",  # MM/DD/YYYY or DD/MM/YYYY
+        ],
+        "datetime": [
+            "2022-01-05T13:16:30.1000005",  # too many decimal points
+            "2022-01-05T13:16:30U",  # time zone too short
+            "2022-01-05T13:16:30UTCUTC",  # time zone too long
+            "2022-01-05T34:10:10",  # invalid time
+        ],
+        "time": [
+            "34:10:10",  # invalid time
+            "24:00:00",  # should be 00:00:00
+            "00:60:00",  # should be 01:00:00
+            "00:00:60",  # should be 00:01:00
+            "01:23",     # lacks either hours or seconds
+        ],
+        "unit": [],
+        "stimuli_relative": [
+            "/path/with/starting/slash/file.txt",
+            "stimuli/path/file.txt",
+        ],
+        "dataset_relative": [
+            "/path/with/starting/slash/file.txt",
+        ],
+        "participant_relative": [
+            "/path/with/starting/slash/file.txt",
+            "sub-01/path/file.txt",
+        ],
+        "rrid": [
+            "RRID:",  # empty one
+        ],
+        "uri": [
+            "ftp://"  # lacks anything but protocol
+        ],
+        "bids_uri": [],
+    }
+    for pattern, test_list in BAD_PATTERNS.items():
+        pattern_format = schema_obj["objects"]["formats"][pattern]["pattern"]
+        search_pattern = f"^{pattern_format}$"
+        search = re.compile(search_pattern)
+        for test_string in test_list:
+            assert not bool(search.fullmatch(test_string))