Additional rules

bids-standard · May 26, 2020 · eb23b96 · eb23b96
1 parent 19c478f
commit eb23b96
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Showing 4 changed files with 155 additions and 34 deletions.
diff --git a/bids-validator/bids_validator/rules/file_level_rules.json b/bids-validator/bids_validator/rules/file_level_rules.json
@@ -236,7 +236,7 @@
   "pet_blood": {
     "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)pet\\/(sub-[a-zA-Z0-9]+)_(?:(ses-[a-zA-Z0-9]+))|((@@@_pet_ext_@@@))$",
     "tokens": {
-      "@@@_pet_ext_@@@": ["_pet-blood\\.nii\\.json"]
+      "@@@_pet_ext_@@@": ["_blood\\.nii\\.json"]
     }
   },
 
@@ -250,7 +250,7 @@
   "pet_blood_data": {
     "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)pet\\/(sub-[a-zA-Z0-9]+)_(?:(ses-[a-zA-Z0-9]+))|((@@@_pet_ext_@@@))$",
     "tokens": {
-      "@@@_pet_ext_@@@": ["_pet-blood\\.tsv"]
+      "@@@_pet_ext_@@@": ["_blood\\.tsv"]
     }
   },
 

diff --git a/bids-validator/validators/json/json.js b/bids-validator/validators/json/json.js
@@ -107,8 +107,6 @@ const selectSchema = file => {
       file.name.endsWith('coordsystem.json')
     ) {
       schema = require('./schemas/coordsystem_eeg.json')
-    } else if (file.name.endsWith('pet_blood.json')) {
-      schema = require('./schemas/pet_blood.json')
     } else if (file.name.endsWith('pet.json')) {
       schema = require('./schemas/pet.json')
     }

diff --git a/...or/validators/json/schemas/pet_blood.json → ...validators/json/schemas/DELETE_LATER.json b/...or/validators/json/schemas/pet_blood.json → ...validators/json/schemas/DELETE_LATER.json
diff --git a/bids-validator/validators/json/schemas/pet.json b/bids-validator/validators/json/schemas/pet.json
@@ -24,16 +24,9 @@
     "PharmaceuticalDoseTimeUnits": { "type": "string", "minLength": 1 },
 
     "InjectedRadioactivity": { "type": "number" },
-    "InjectedRadioActivityUnit": {
-      "type": "string",
-      "minLength": 1,
-      "enum": ["megabecquerel"]
-    },
+    "InjectedRadioactivityUnit": { "type": "string", "minLength": 1 },
     "InjectedMass": { "type": "number" },
-    "InjectedMassUnit": {
-      "type": "string",
-      "minLength": 1
-    },
+    "InjectedMassUnit": { "type": "string", "minLength": 1 },
     "InjectedMassPerWeight": { "type": "number" },
     "InjectedMassPerWeightUnit": {
       "type": "string",
@@ -171,26 +164,132 @@
       "items": { "type": "number" }
     },
 
-    "BloodAvail": { "type": "boolean" }
-  },
-  "allOf": [
-    {
-      "if": {
-        "properties": {
-          "BloodAvail": {
-            "enum": [true]
-          }
-        }
-      },
-      "then": {
-        "required": [
-          "PlasmaAvail",
-          "MetaboliteAvail",
-          "ContinousBloodAvail",
-          "DiscreteBloodAvail"
-        ]
+    "MetaboliteAvail": {
+      "default": false,
+      "type": "boolean"
+    },
+    "PlasmaAvail": {
+      "default": false,
+      "type": "boolean"
+    },
+    "ContinousBloodAvail": {
+      "default": false,
+      "type": "boolean"
+    },
+    "DiscreteBloodAvail": {
+      "default": false,
+      "type": "boolean"
+    },
+
+    "Modality": { "type": "string", "minLength": 1 },
+    "PlasmaType": { "type": "string", "minLength": 1 },
+    "FreeFraction": {
+      "type": "number",
+      "min": 0,
+      "max": 1
+    },
+    "FreeFractionMethod": { "type": "string", "minLength": 1 },
+    "PlasmaTimeZero": {
+      "type": "string",
+      "pattern": "^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$"
+    },
+    "PlasmaDecayCorrected": { "type": "boolean" },
+    "PlasmaDecayCorrectionTime": {
+      "type": "string",
+      "pattern": "^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$"
+    },
+    "PlasmaSampleTime": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "PlasmaSampleTimeUnits": { "type": "string", "minLength": 1 },
+    "PlasmaActivity": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "PlasmaActivityUnits": { "type": "string", "minLength": 1 },
+
+    "MetaboliteType": { "type": "string", "minLength": 1 },
+    "MetaboliteMethod": { "type": "string", "minLength": 1 },
+    "MetaboliteTimeZero": {
+      "type": "string",
+      "pattern": "^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$"
+    },
+    "MetaboliteSampleTime": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "MetaboliteSampleTimeUnits": { "type": "string", "minLength": 1 },
+    "MetaboliteParentFraction": {
+      "type": "array",
+      "items": {
+        "type": "number",
+        "min": 0,
+        "max": 1
       }
     },
+    "MetaboliteParentFractionUnits": { "type": "string", "minLength": 1 },
+    "MetabolitePolar": { "type": "array", "items": { "type": "number" } },
+    "MetabolitePolarUnits": { "type": "string", "minLength": 1 },
+    "MetaboliteLipophilic": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "MetaboliteLipophilicUnits": { "type": "string", "minLength": 1 },
+
+    "Haematocrit": { "type": "string", "minLength": 1 },
+    "BloodDensity": { "type": "string", "minLength": 1 },
+    "BloodDensityUnits": { "type": "string", "minLength": 1 },
+    "BloodDiscreteTimeZero": {
+      "type": "string",
+      "pattern": "^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$"
+    },
+    "BloodDiscreteDecayCorrected": { "type": "boolean" },
+    "BloodDiscreteDecayCorrectionTime": {
+      "type": "string",
+      "pattern": "^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$"
+    },
+    "BloodDiscreteType": { "type": "string", "minLength": 1 },
+    "BloodDiscreteSampleTime": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "BloodDiscreteSampleTimeUnits": { "type": "string", "minLength": 1 },
+    "BloodDiscreteActivity": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "BloodDiscreteActivityUnits": { "type": "string", "minLength": 1 },
+
+    "WithdrawalRate": { "type": "string", "minLength": 1 },
+    "WithdrawalRateUnits": { "type": "string", "minLength": 1 },
+    "TubingLength": { "type": "string", "minLength": 1 },
+    "TubingLengthUnits": { "type": "string", "minLength": 1 },
+    "DispersionCorrected": { "type": "boolean" },
+    "DispersionConstant": { "type": "string", "minLength": 1 },
+    "DispersionConstantUnits": { "type": "string", "minLength": 1 },
+    "BloodContinuousTimeZero": {
+      "type": "string",
+      "pattern": "^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$"
+    },
+    "BloodContinuousDecayCorrected": { "type": "boolean" },
+    "BloodContinuousDecayCorrectionTime": {
+      "type": "string",
+      "pattern": "^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$"
+    },
+    "BloodContinuousType": { "type": "string", "minLength": 1 },
+    "BloodContinuousSampleTime": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "BloodContinuousSampleTimeUnits": { "type": "string", "minLength": 1 },
+    "BloodContinuousActivity": {
+      "type": "array",
+      "items": { "type": "number" }
+    },
+    "BloodContinuousActivityUnits": { "type": "string", "minLength": 1 }
+  },
+  "allOf": [
     {
       "if": {
         "properties": {
@@ -252,13 +351,16 @@
     "ReconFilterSize",
     "AttenuationCorrection",
 
-    "BloodAvail"
+    "MetaboliteAvail",
+    "PlasmaAvail",
+    "ContinousBloodAvail",
+    "DiscreteBloodAvail"
   ],
   "dependencies": {
     "TracerMolecularWeight": ["TracerMolecularWeightUnit"],
     "BodyWeight": ["BodyWeightUnit"],
 
-    "InjectedRadioactivity": ["InjectedRadioActivityUnit"],
+    "InjectedRadioactivity": ["InjectedRadioactivityUnit"],
     "InjectedMass": ["InjectedMassUnit"],
     "InjectedMassPerWeight": ["InjectedMassPerWeightUnit"],
     "MolarActivity": ["MolarActivityUnit"],
@@ -274,6 +376,27 @@
     "ReconMethodParameterLabels": [
       "ReconMethodParameterUnit",
       "ReconMethodParameterValues"
-    ]
+    ],
+
+    "PlasmaDecayCorrected": ["PlasmaDecayCorrectionTime"],
+    "PlasmaSampleTime": ["PlasmaSampleTimeUnits"],
+    "PlasmaActivity": ["PlasmaActivityUnits"],
+
+    "MetaboliteSampleTime": ["MetaboliteSampleTimeUnits"],
+    "MetaboliteParentFraction": ["MetaboliteParentFractionUnits"],
+    "MetabolitePolar": ["MetabolitePolarUnits"],
+    "MetaboliteLipophilic": ["MetaboliteLipophilicUnits"],
+
+    "BloodDensity": ["BloodDensityUnits"],
+    "BloodDiscreteDecayCorrected": ["BloodDiscreteDecayCorrectionTime"],
+    "BloodDiscreteSampleTime": ["BloodDiscreteSampleTimeUnits"],
+    "BloodDiscreteActivity": ["BloodDiscreteActivityUnits"],
+
+    "WithdrawalRate": ["WithdrawalRateUnits"],
+    "TubingLength": ["TubingLengthUnits"],
+    "DispersionCorrected": ["DispersionConstant", "DispersionConstantUnits"],
+    "BloodContinuousSampleTime": ["BloodContinuousSampleTimeUnits"],
+    "BloodContinuousActivity": ["BloodContinuousActivityUnits"],
+    "BloodContinuousDecayCorrected": ["BloodContinuousDecayCorrectionTime"]
   }
 }