Freemabd/dt 941 (#1111)

* DT-941 adding config for fitbit device

* DT-941 fixing config for CT

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbit/selector.json

@@ -1,10 +1,10 @@
 {
   "name": "tanagra-fitbit",
-  "displayName": "Fitbit data",
+  "displayName": "Has Any Fitbit Data",
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitActivitySummary/selector.json

@@ -1,10 +1,10 @@
 {
   "name": "tanagra-fitbit-activity-summary",
-  "displayName": "Fitbit Activity Summary",
+  "displayName": "Has Fitbit Activity Summary",
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitDevice/fitbitDevice.json

@@ -0,0 +1,3 @@
+{
+  "attribute": "has_fitbit_device"
+}

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitDevice/selector.json

@@ -0,0 +1,15 @@
+{
+  "name": "tanagra-fitbit-device",
+  "displayName": "Has Fitbit Device",
+  "isEnabledForCohorts": true,
+  "isEnabledForDataFeatureSets": false,
+  "display": {
+    "category": "Wearables",
+    "tags": null
+  },
+  "filterBuilder": "core.PrimaryEntityFilterBuilder",
+  "plugin": "attribute",
+  "pluginConfig": null,
+  "pluginConfigFile": "fitbitDevice.json",
+  "modifiers": null
+}

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitHeartRateLevel/selector.json

@@ -1,10 +1,10 @@
 {
   "name": "tanagra-fitbit-heart-rate-level",
-  "displayName": "Fitbit Heart Rate Minute Level",
+  "displayName": "Has Fitbit Heart Rate Minute Level",
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitHeartRateSummary/selector.json

@@ -1,10 +1,10 @@
 {
   "name": "tanagra-fitbit-heart-rate-summary",
-  "displayName": "Fitbit Heart Rate Summary",
+  "displayName": "Has Fitbit Heart Rate Summary",
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitPlusDevice/fitbitPlusDevice.json

@@ -0,0 +1,3 @@
+{
+  "attribute": "has_fitbit_plus_device"
+}

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitPlusDevice/selector.json

@@ -0,0 +1,15 @@
+{
+  "name": "tanagra-fitbit-plus-device",
+  "displayName": "Has Any Fitbit Data Plus Device",
+  "isEnabledForCohorts": true,
+  "isEnabledForDataFeatureSets": false,
+  "display": {
+    "category": "Wearables",
+    "tags": null
+  },
+  "filterBuilder": "core.PrimaryEntityFilterBuilder",
+  "plugin": "attribute",
+  "pluginConfig": null,
+  "pluginConfigFile": "fitbitPlusDevice.json",
+  "modifiers": null
+}

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitSleepDailySummary/selector.json

@@ -1,10 +1,10 @@
 {
   "name": "tanagra-fitbit-sleep-daily-summary",
-  "displayName": "Fitbit Sleep Daily Summary",
+  "displayName": "Has Fitbit Sleep Daily Summary",
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitSleepLevel/selector.json

@@ -1,10 +1,10 @@
 {
   "name": "tanagra-fitbit-sleep-level",
-  "displayName": "Fitbit Sleep Level",
+  "displayName": "Has Fitbit Sleep Level",
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/fitbitStepsIntraday/selector.json

@@ -1,10 +1,10 @@
 {
   "name": "tanagra-fitbit-steps-intraday",
-  "displayName": "Fitbit Steps Intraday",
+  "displayName": "Has Fitbit Steps Intraday",
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/pregnant/pregnant.json

@@ -1,8 +1,3 @@
 {
-  "entity": "pregnant",
-  "valueConfigs": [
-    {
-      "attribute": "pregnant_at_enrollment"
-    }
-  ]
+  "attribute": "has_pregnant_at_enrollment"
 }

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/pregnant/selector.json

@@ -7,8 +7,8 @@
     "category": "Physical Measurements",
     "tags": null
   },
-  "filterBuilder": "core.MultiAttributeFilterBuilder",
-  "plugin": "multiAttribute",
+  "filterBuilder": "core.PrimaryEntityFilterBuilder",
+  "plugin": "attribute",
   "pluginConfig": null,
   "pluginConfigFile": "pregnant.json",
   "modifiers": null

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/wearConsent/selector.json

@@ -4,7 +4,7 @@
   "isEnabledForCohorts": true,
   "isEnabledForDataFeatureSets": false,
   "display": {
-    "category": "Fitbit",
+    "category": "Wearables",
     "tags": null
   },
   "filterBuilder": "core.PrimaryEntityFilterBuilder",

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/wheelchair/selector.json

@@ -7,8 +7,8 @@
     "category": "Physical Measurements",
     "tags": null
   },
-  "filterBuilder": "core.MultiAttributeFilterBuilder",
-  "plugin": "multiAttribute",
+  "filterBuilder": "core.PrimaryEntityFilterBuilder",
+  "plugin": "attribute",
   "pluginConfig": null,
   "pluginConfigFile": "wheelchair.json",
   "modifiers": null

underlay/src/main/resources/config/criteria/aouRT/criteriaselector/wheelchair/wheelchair.json

@@ -1,8 +1,3 @@
 {
-  "entity": "wheelchair",
-  "valueConfigs": [
-    {
-      "attribute": "wheelchair_at_enrollment"
-    }
-  ]
+  "attribute": "has_wheelchair_at_enrollment"
 }

underlay/src/main/resources/config/criteria/aouRT/prepackagedcriteria/_fitbit_actvity_summary_id/prepackaged.json → underlay/src/main/resources/config/criteria/aouRT/prepackagedcriteria/_fitbit_activity_summary_id/prepackaged.json

@@ -1,5 +1,5 @@
 {
-  "name": "_fitbit_actvity_summary_id",
+  "name": "_fitbit_activity_summary_id",
   "displayName": "Fitbit Activity Summary",
   "criteriaSelector": "outputUnfiltered",
   "pluginDataFile": "fitbitActvitySummaryId.json"

underlay/src/main/resources/config/criteria/aouRT/prepackagedcriteria/_fitbit_device_id/fitbitDeviceId.json

@@ -0,0 +1,5 @@
+{
+  "entities": [
+    "wearableDevice"
+  ]
+}

underlay/src/main/resources/config/criteria/aouRT/prepackagedcriteria/_fitbit_device_id/prepackaged.json

@@ -0,0 +1,6 @@
+{
+  "name": "_fitbit_device_id",
+  "displayName": "Fitbit Device",
+  "criteriaSelector": "outputUnfiltered",
+  "pluginDataFile": "fitbitDeviceId.json"
+}

underlay/src/main/resources/config/datamapping/aouCT/entity/person/all.sql

@@ -54,9 +54,14 @@ SELECT p.person_id,
            WHEN sds.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_sleep_daily_summary,
        CASE
            WHEN sl.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_sleep_level,
+        CASE
+           WHEN dev.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_device,
        CASE
            WHEN asum.person_id IS NULL AND hrml.person_id IS NULL AND hrs.person_id IS NULL
            AND si.person_id IS NULL AND sds.person_id IS NULL AND sl.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit,
+       CASE
+           WHEN asum.person_id IS NULL AND hrml.person_id IS NULL AND hrs.person_id IS NULL
+           AND si.person_id IS NULL AND sds.person_id IS NULL AND sl.person_id IS NULL AND dev.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_plus_device,
        CASE
            WHEN wgv.sample_name IS NULL THEN FALSE ELSE TRUE END has_whole_genome_variant,
        CASE
@@ -71,6 +76,10 @@ SELECT p.person_id,
            WHEN ehr.person_id IS NULL THEN FALSE ELSE TRUE END has_ehr_data,
        CASE
            WHEN pm.person_id IS NULL THEN FALSE ELSE TRUE END has_pm_data,
+       CASE
+           WHEN pregnant.person_id IS NULL THEN FALSE ELSE TRUE END has_pregnant_at_enrollment,
+       CASE
+           WHEN wheelchair.person_id IS NULL THEN FALSE ELSE TRUE END has_wheelchair_at_enrollment,
        CASE
            WHEN d.death_date is null THEN FALSE ELSE TRUE END is_deceased
 FROM `${omopDataset}.person` p
@@ -85,6 +94,7 @@ LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.heart_rate_summary`) h
 LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.steps_intraday`) si ON (p.person_id = si.person_id)
 LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_daily_summary`) sds ON (p.person_id = sds.person_id)
 LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_level`) sl ON (p.person_id = sl.person_id)
+LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.device`) dev ON (p.person_id = dev.person_id)
 LEFT JOIN (SELECT DISTINCT sample_name FROM `${omopDataset}.prep_wgs_metadata`) wgv ON (CAST(p.person_id AS STRING) = wgv.sample_name)
 LEFT JOIN (SELECT DISTINCT sample_name FROM `${omopDataset}.prep_microarray_metadata`) mad ON (CAST(p.person_id AS STRING) = mad.sample_name)
 LEFT JOIN (SELECT DISTINCT sample_name FROM `${omopDataset}.prep_longreads_metadata`) lrwgv ON (CAST(p.person_id AS STRING) = lrwgv.sample_name)
@@ -126,5 +136,13 @@ LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.measurement`
                  AND domain_id = 'Measurement'
            )
 ) pm ON (p.person_id = pm.person_id)
+LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.observation`
+           WHERE observation_source_concept_id = 903120
+             AND value_as_concept_id = 45877994
+) pregnant ON (p.person_id = pregnant.person_id)
+LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.measurement`
+           WHERE measurement_source_concept_id = 903111
+             AND value_as_concept_id = 4023190
+) wheelchair ON (p.person_id = wheelchair.person_id)
 LEFT JOIN (SELECT person_id, max(death_date) as death_date FROM `${omopDataset}.death` GROUP BY person_id) d
 ON (p.person_id = d.person_id)

underlay/src/main/resources/config/datamapping/aouCT/entity/person/entity.json

@@ -57,13 +57,17 @@
     { "name": "has_fitbit_sleep_daily_summary", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_fitbit_sleep_level", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_fitbit", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_fitbit_device", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_fitbit_plus_device", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_array_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_whole_genome_variant", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_lr_whole_genome_variant", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_structural_variant_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_wear_consent", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_ehr_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_pm_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_pregnant_at_enrollment", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_wheelchair_at_enrollment", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "is_deceased", "dataType": "BOOLEAN", "isSuppressedForExport": true }
   ],
   "idAttribute": "id",

underlay/src/main/resources/config/datamapping/aouRT/entity/person/all.sql

@@ -50,15 +50,24 @@ SELECT p.person_id,
            WHEN sds.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_sleep_daily_summary,
        CASE
            WHEN sl.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_sleep_level,
+        CASE
+           WHEN dev.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_device,
        CASE
            WHEN asum.person_id IS NULL AND hrml.person_id IS NULL AND hrs.person_id IS NULL
            AND si.person_id IS NULL AND sds.person_id IS NULL AND sl.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit,
+       CASE
+           WHEN asum.person_id IS NULL AND hrml.person_id IS NULL AND hrs.person_id IS NULL
+           AND si.person_id IS NULL AND sds.person_id IS NULL AND sl.person_id IS NULL AND dev.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_plus_device,
        CASE
            WHEN ws.person_id IS NULL THEN FALSE ELSE TRUE END has_wear_consent,
        CASE
            WHEN ehr.person_id IS NULL THEN FALSE ELSE TRUE END has_ehr_data,
        CASE
            WHEN pm.person_id IS NULL THEN FALSE ELSE TRUE END has_pm_data,
+       CASE
+           WHEN pregnant.person_id IS NULL THEN FALSE ELSE TRUE END has_pregnant_at_enrollment,
+       CASE
+           WHEN wheelchair.person_id IS NULL THEN FALSE ELSE TRUE END has_wheelchair_at_enrollment,
        CASE
            WHEN d.death_date is null THEN FALSE ELSE TRUE END is_deceased
 FROM `${omopDataset}.person` p
@@ -73,6 +82,7 @@ LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.heart_rate_summary`) h
 LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.steps_intraday`) si ON (p.person_id = si.person_id)
 LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_daily_summary`) sds ON (p.person_id = sds.person_id)
 LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_level`) sl ON (p.person_id = sl.person_id)
+LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.device`) dev ON (p.person_id = dev.person_id)
 LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.wear_study`) ws ON (p.person_id = ws.person_id)
 LEFT JOIN (SELECT DISTINCT person_id FROM`${omopDataset}.measurement` as a
             LEFT JOIN`${omopDataset}.measurement_ext` as b on a.measurement_id = b.measurement_id
@@ -110,5 +120,13 @@ LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.measurement`
                  AND domain_id = 'Measurement'
            )
 ) pm ON (p.person_id = pm.person_id)
+LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.observation`
+           WHERE observation_source_concept_id = 903120
+             AND value_as_concept_id = 45877994
+) pregnant ON (p.person_id = pregnant.person_id)
+LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.measurement`
+           WHERE measurement_source_concept_id = 903111
+             AND value_as_concept_id = 4023190
+) wheelchair ON (p.person_id = wheelchair.person_id)
 LEFT JOIN (SELECT person_id, max(death_date) as death_date FROM `${omopDataset}.death` GROUP BY person_id) d
 ON (p.person_id = d.person_id)

underlay/src/main/resources/config/datamapping/aouRT/entity/person/entity.json

@@ -57,9 +57,13 @@
     { "name": "has_fitbit_sleep_daily_summary", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_fitbit_sleep_level", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_fitbit", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_fitbit_device", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_fitbit_plus_device", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_wear_consent", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_ehr_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "has_pm_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_pregnant_at_enrollment", "dataType": "BOOLEAN", "isSuppressedForExport": true },
+    { "name": "has_wheelchair_at_enrollment", "dataType": "BOOLEAN", "isSuppressedForExport": true },
     { "name": "is_deceased", "dataType": "BOOLEAN", "isSuppressedForExport": true }
   ],
   "idAttribute": "id",

underlay/src/main/resources/config/datamapping/aouRT/entity/wearableDevice/all.sql

@@ -0,0 +1,12 @@
+SELECT
+    row_id,
+    person_id,
+    device_id,
+    device_date,
+    battery,
+    battery_level,
+    device_version,
+    device_type,
+    TIMESTAMP(last_sync_time) AS last_sync_time,
+    src_id
+FROM `${omopDataset}.device`