Re-apply referencing IEEE schemas (#28)

* Revert "Revert "Feature/reference ieee schemas""

This reverts commit f25a749.

* Use versions of dependencies known to work

.github/workflows/validator.yaml

@@ -39,7 +39,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install requests "jsonschema[format]"
+        pip install -r requirements.txt
 
     - name: Run validator
       run: |

schema/omh/area-unit-value-1.1.json

@@ -0,0 +1,39 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "https://w3id.org/openmhealth/schemas/omh/area-unit-value-1.1.json",
+    "type": "object",
+    "description": "This schema represents an area (measure of a surface)",
+    "references": [
+        {
+            "description": "The SNOMED code represents Area",
+            "url": "http://purl.bioontology.org/ontology/SNOMEDCT/42798000"
+        }
+    ],
+    "allOf": [
+        {
+            "$ref": "https://w3id.org/ieee/ieee-1752-schema/unit-value-1.0.json"
+        },
+        {
+            "properties": {
+                "unit": {
+                    "references": [
+                        {
+                            "description": "The unit of measure of the element. Basic unit is meter (m). Allowed values are drawn from the SI Area Units and English Area Units Common Synonyms (non-UCUM). The valid UCUM code is different for square inch ([sin_i]), square foot ([sft_i]), square yard ([syd_i]).",
+                            "url": "http://download.hl7.de/documents/ucum/ucumdata.html"
+                        }
+                    ],
+                    "enum": [
+                        "mm^2",
+                        "cm^2",
+                        "m^2",
+                        "km^2",
+                        "in^2",
+                        "ft^2",
+                        "yd^2",
+                        "mi^2"
+                    ]
+                }
+            }
+        }
+    ]
+}

schema/omh/blood-pressure-4.0.json

@@ -0,0 +1,66 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "https://w3id.org/openmhealth/schemas/omh/blood-pressure-4.0.json",
+    "description": "This schema represents a person's blood pressure as a combination of systolic and diastolic blood pressure.",
+    "type": "object",
+    "references": [
+        {
+            "description": "The SNOMED codes represents Blood pressure (observable entity)",
+            "url": "http://purl.bioontology.org/ontology/SNOMEDCT/75367002"
+        }
+    ],
+    "definitions": {
+        "systolic_blood_pressure": {
+            "$ref": "systolic-blood-pressure-1.x.json"
+        },
+        "diastolic_blood_pressure": {
+            "$ref": "diastolic-blood-pressure-1.x.json"
+        },
+        "time_frame": {
+            "$ref": "https://w3id.org/ieee/ieee-1752-schema/time-frame-1.0.json"
+        },
+        "body_posture": {
+            "$ref": "https://w3id.org/ieee/ieee-1752-schema/body-posture-1.0.json"
+        },
+        "body_location": {
+            "$ref": "body-location-1.x.json"
+        },
+        "temporal_relationship_to_physical_activity": {
+            "$ref": "temporal-relationship-to-physical-activity-1.x.json"
+        },
+        "descriptive_statistic": {
+            "$ref": "https://w3id.org/ieee/ieee-1752-schema/descriptive-statistic-1.0.json"
+        }
+    },
+
+    "properties": {
+        "systolic_blood_pressure": {
+            "$ref": "#/definitions/systolic_blood_pressure"
+        },
+        "diastolic_blood_pressure": {
+            "$ref": "#/definitions/diastolic_blood_pressure"
+        },
+        "effective_time_frame": {
+            "$ref": "#/definitions/time_frame"
+        },
+        "body_posture": {
+            "$ref": "#/definitions/body_posture"
+        },
+        "descriptive_statistic": {
+            "$ref": "#/definitions/descriptive_statistic"
+        },
+        "measurement_location": {
+            "description": "The location on the body where the blood pressure measuring device is placed for measurement.",
+            "$ref": "#/definitions/body_location"
+        },
+        "temporal_relationship_to_physical_activity": {
+            "$ref": "#/definitions/temporal_relationship_to_physical_activity"
+        }
+    },
+
+    "required": [
+        "systolic_blood_pressure",
+        "diastolic_blood_pressure",
+        "effective_time_frame"
+    ]
+}

schema/omh/blood-pressure-4.x.json

@@ -0,0 +1 @@
+blood-pressure-4.0.json

schema/omh/body-posture-1.0.json

@@ -1,6 +1,10 @@
 {
     "$schema": "http://json-schema.org/draft-04/schema#",
-
+    "deprecation": {
+        "reason": "This schema is now deprecated, in favor of the IEEE 1752.1 schema of the same name.",
+        "supersededBy": "https://w3id.org/ieee/ieee-1752-schema/body-posture.json",
+        "date": "2022-12-01"
+    },
     "type": "string",
     "description": "The posture of the subject (for example, during a clinical measurement). This value set is not exhaustive.",
     "references": [

schema/omh/physical-activity-1.2.json

@@ -1,6 +1,10 @@
 {
     "$schema": "http://json-schema.org/draft-04/schema#",
-
+    "deprecation": {
+        "reason": "This schema is now deprecated, in favor of the IEEE 1752.1 schema with the same name.",
+        "supersededBy": "https://w3id.org/ieee/ieee-1752-schema/physical-activity.json",
+        "date": "2022-12-01"
+    },
     "description": "This schema represents a single episode of physical activity.",
     "type": "object",
     "references": [

schema/omh/step-count-3.0.json

@@ -1,6 +1,10 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-
+    "deprecation": {
+        "reason": "This schema is now deprecated, in favor of the IEEE 1752.1 physical-activity schema which models also number of steps.",
+        "supersededBy": "https://w3id.org/ieee/ieee-1752-schema/physical-activity.json",
+        "date": "2022-12-01"
+    },
     "description": "This schema represents number of steps.",
 
     "type": "object",

schema/omh/time-frame-1.0.json

@@ -1,6 +1,10 @@
 {
     "$schema": "http://json-schema.org/draft-04/schema#",
-
+    "deprecation": {
+        "reason": "This schema is now deprecated, in favor of the IEEE 1752.1 schema of the same name.",
+        "supersededBy": "https://w3id.org/ieee/ieee-1752-schema/time-frame.json",
+        "date": "2022-12-01"
+    },
     "description": "This schema describes a time frame as a point in time or a time interval.",
 
     "type": "object",

schema/omh/time-interval-1.0.json

@@ -1,6 +1,10 @@
 {
     "$schema": "http://json-schema.org/draft-04/schema#",
-
+    "deprecation": {
+        "reason": "This schema is now deprecated, in favor of the IEEE 1752.1 schema of the same name.",
+        "supersededBy": "https://w3id.org/ieee/ieee-1752-schema/time-interval.json",
+        "date": "2022-12-01"
+    },
     "description": "This schema describes an interval of time. In the absence of a precise start and/or end time, the time interval can be described as a date + a part of the day (morning, afternoon, evening, night). No commitments are made as to whether the start or end time point itself is included in the interval (i.e., whether the defined interval includes the boundary point(s) or not).",
     "type": "object",
 

test-data-validator/README.md

@@ -9,8 +9,7 @@ You'll need [Python 3.7](https://www.python.org/downloads/) or later.
 You'll also need the [requests](https://pypi.org/project/requests/) and [jsonschema](https://pypi.org/project/jsonschema/) Python packages. Note that `jsonschema` depends on [format checkers](https://python-jsonschema.readthedocs.io/en/stable/validate/#validating-formats). You can install the format checkers with `jsonschema` by using the following commands:
 
 ```sh
-pip install requests
-pip install "jsonschema[format]"
+pip install -r requirements.txt
 ```
 
 > If you have both Python 2 and Python 3, your Python 3 command may be called `python3` and your Python 3 package installer command may be called `pip3`. Please use the appropriate Python 3 commands for your system. 

test-data-validator/requirements.txt

@@ -0,0 +1,2 @@
+jsonschema[format]==4.17.3
+requests==2.31.0

test-data/ieee/ambient-sound/1.0/shouldFail/invalid-ambient-sound.json

@@ -0,0 +1,9 @@
+{
+    "ambient_sound": {
+        "value": 75,
+        "unit": "deciB"
+    },
+    "effective_time_frame": {
+        "date_time": "2019-02-05T06:00:00Z"
+    }
+}

test-data/ieee/body-posture/1.0/shouldFail/invalid-posture.json

@@ -0,0 +1 @@
+"stnding"

test-data/ieee/body-posture/1.0/shouldPass/valid-posture.json

@@ -0,0 +1 @@
+"semi-recumbent"

test-data/ieee/time-frame/1.0/shouldFail/empty-document.json

@@ -0,0 +1 @@
+{}

test-data/ieee/time-frame/1.0/shouldFail/time-interval-and-date-time.json

@@ -0,0 +1,10 @@
+{
+    "date_time": "2013-02-05T07:25:00.123Z",
+    "time_interval": {
+        "duration": {
+            "value": 10,
+            "unit": "d"
+        },
+        "end_date_time": "2013-02-05T07:35:00Z"
+    }
+}

test-data/ieee/time-interval/1.0/shouldFail/duration-only.json

@@ -0,0 +1,6 @@
+{
+    "duration": {
+        "unit": "h",
+        "value": 7.6
+    }
+}

test-data/ieee/time-interval/1.0/shouldFail/empty-document.json

@@ -0,0 +1 @@
+{}

test-data/ieee/time-interval/1.0/shouldFail/end-time-only.json

@@ -0,0 +1,3 @@
+{
+    "end_date_time": "2013-02-05T07:25:00Z"
+}

test-data/ieee/time-interval/1.0/shouldFail/start-time-only.json

@@ -0,0 +1,3 @@
+{
+    "start_date_time": "2013-02-05T07:25:00Z"
+}

test-data/omh/area-unit-value/1.1/shouldFail/invalid-unit.json

@@ -0,0 +1,4 @@
+{
+    "unit": "foo",
+    "value": 7.6
+}

test-data/omh/area-unit-value/1.1/shouldFail/unit-only.json

@@ -0,0 +1,3 @@
+{
+    "unit": "m^2"
+}

test-data/omh/area-unit-value/1.1/shouldFail/value-only.json

@@ -0,0 +1,3 @@
+{
+    "value": 10
+}

test-data/omh/area-unit-value/1.1/shouldPass/positive-value.json

@@ -0,0 +1,4 @@
+{
+    "unit": "m^2",
+    "value": 7.6
+}

test-data/omh/blood-pressure/4.0/shouldFail/empty-document.json

@@ -0,0 +1 @@
+{}

test-data/omh/blood-pressure/4.0/shouldFail/invalid-pa-value.json

@@ -0,0 +1,14 @@
+{
+    "systolic_blood_pressure": {
+        "value": 115,
+        "unit": "mmHg"
+    },
+    "diastolic_blood_pressure": {
+        "value": 60,
+        "unit": "mmHg"
+    },
+    "effective_time_frame": {
+        "date_time": "2020-02-05T07:25:00-08:00"
+    },
+    "temporal_relationship_to_physical_activity": "rest"
+}

test-data/omh/blood-pressure/4.0/shouldFail/invalid-timeframe-format.json

@@ -0,0 +1,17 @@
+{
+    "systolic_blood_pressure": {
+        "value": 115,
+        "unit": "mmHg"
+    },
+    "diastolic_blood_pressure": {
+        "value": 60,
+        "unit": "mmHg"
+    },
+    "effective_time_frame": {
+        "time_interval": {
+            "date": "2013-02-05",
+            "part_of_day": "morning"
+        }
+    },
+    "temporal_relationship_to_physical_activity": "at rest"
+}

test-data/omh/blood-pressure/4.0/shouldFail/invalid-unit.json

@@ -0,0 +1,13 @@
+{
+    "systolic_blood_pressure": {
+        "value": 115,
+        "unit": "mmH"
+    },
+    "diastolic_blood_pressure": {
+        "value": 60,
+        "unit": "mmHg"
+    },
+    "effective_time_frame": {
+        "date_time": "2020-02-05T07:25:00-08:00"
+    }
+}

test-data/omh/blood-pressure/4.0/shouldPass/blood-pressure-only.json

@@ -0,0 +1,13 @@
+{
+    "systolic_blood_pressure": {
+        "value": 115,
+        "unit": "mmHg"
+    },
+    "diastolic_blood_pressure": {
+        "value": 60,
+        "unit": "mmHg"
+    },
+    "effective_time_frame": {
+        "date_time": "2020-02-05T07:25:00-08:00"
+    }
+}

test-data/omh/blood-pressure/4.0/shouldPass/with-descriptive-statistic.json

@@ -0,0 +1,19 @@
+{
+    "systolic_blood_pressure": {
+        "value": 160,
+        "unit": "mmHg"
+    },
+    "diastolic_blood_pressure": {
+        "value": 60,
+        "unit": "mmHg"
+    },
+    "effective_time_frame": {
+        "time_interval": {
+            "start_date_time": "2020-02-05T07:00:00-08:00",
+            "end_date_time": "2020-02-12T07:00:00-08:00"
+        }
+    },
+    "body_posture": "sitting",
+    "measurement_location": "left wrist",
+    "descriptive_statistic": "maximum"
+}

test-data/omh/blood-pressure/4.0/shouldPass/with-posture-and-location.json

@@ -0,0 +1,15 @@
+{
+    "systolic_blood_pressure": {
+        "value": 140,
+        "unit": "mmHg"
+    },
+    "diastolic_blood_pressure": {
+        "value": 60,
+        "unit": "mmHg"
+    },
+    "body_posture": "sitting",
+    "measurement_location": "left upper arm",
+    "effective_time_frame": {
+        "date_time": "2020-02-05T07:25:00-08:00"
+    }
+}

test-data/omh/blood-pressure/4.0/shouldPass/with-posture-location-relation.json

@@ -0,0 +1,16 @@
+{
+    "systolic_blood_pressure": {
+        "value": 125,
+        "unit": "mmHg"
+    },
+    "diastolic_blood_pressure": {
+        "value": 60,
+        "unit": "mmHg"
+    },
+    "body_posture": "sitting",
+    "measurement_location": "left wrist",
+    "temporal_relationship_to_physical_activity": "at rest",
+    "effective_time_frame": {
+        "date_time": "2020-02-05T07:25:00-08:00"
+    }
+}