diff --git a/nbri_ehr/resources/queries/ehr_lookups/buildings.js b/nbri_ehr/resources/queries/ehr_lookups/buildings.js index 3fca085..b5e9890 100644 --- a/nbri_ehr/resources/queries/ehr_lookups/buildings.js +++ b/nbri_ehr/resources/queries/ehr_lookups/buildings.js @@ -7,6 +7,19 @@ var LABKEY = require("labkey"); var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); +// Width of ehr_lookups.buildings.name. The description it is derived from is a wider column, so it can overrun the +// key; reject it here rather than letting the database raise an unreadable error. +var MAX_NAME_LENGTH = 100; + +// 'name' is not user editable, so it is absent from the incoming row map and the value this script derives has +// nowhere to land. Declaring it managed reserves a slot so the derived key is persisted. +function managedColumns() { + return { + insert: ["name"], + update: ["name"], + }; +} + function onUpsert(row, oldRow, errors){ if (extraContext.dataSource != "etl") { if (!row.description) { @@ -25,7 +38,19 @@ function onUpsert(row, oldRow, errors){ return; } - row.name = row.description + '-' + row.area; + if (row.description.length > MAX_NAME_LENGTH) { + errors['description'] = 'Description is too long: it becomes the building key, which cannot exceed ' + MAX_NAME_LENGTH + ' characters.'; + return; + } + + // The description alone identifies the building now that the area is no longer folded in, so a duplicate + // would collide on the key. Say so here instead of surfacing a constraint violation on a hidden column. + if (triggerHelper.totalRecords("ehr_lookups", "buildings", "name", row.description) > 0) { + errors['description'] = 'A building described as ' + row.description + ' already exists. Building descriptions must be unique.'; + return; + } + + row.name = row.description; } } } diff --git a/nbri_ehr/resources/queries/ehr_lookups/cage.js b/nbri_ehr/resources/queries/ehr_lookups/cage.js index e19a2b7..0e71832 100644 --- a/nbri_ehr/resources/queries/ehr_lookups/cage.js +++ b/nbri_ehr/resources/queries/ehr_lookups/cage.js @@ -7,6 +7,19 @@ var LABKEY = require("labkey"); var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); +// Width of ehr_lookups.cage.location. The derived key builds on the room key, which is itself derived, so it can +// overrun the column; reject it here rather than letting the database raise an unreadable error. +var MAX_LOCATION_LENGTH = 100; + +// 'location' is not user editable, so it is absent from the incoming row map and the value this script +// derives has nowhere to land. Declaring it managed reserves a slot so the derived key is persisted. +function managedColumns() { + return { + insert: ["location"], + update: ["location"], + }; +} + function onUpsert(row, oldRow, errors){ if (extraContext.dataSource != "etl") { if (!row.location) { @@ -20,9 +33,16 @@ function onUpsert(row, oldRow, errors){ return; } - row.location = row.room; + let location = row.room; if (row.cage) - row.location += '-' + row.cage; + location += '-' + row.cage; + + if (location.length > MAX_LOCATION_LENGTH) { + errors['cage'] = 'Room and cage are too long: they combine to a ' + location.length + ' character location key, which cannot exceed ' + MAX_LOCATION_LENGTH + '.'; + return; + } + + row.location = location; } } } diff --git a/nbri_ehr/resources/queries/ehr_lookups/cage.query.xml b/nbri_ehr/resources/queries/ehr_lookups/cage.query.xml index 97b1549..3d15c46 100644 --- a/nbri_ehr/resources/queries/ehr_lookups/cage.query.xml +++ b/nbri_ehr/resources/queries/ehr_lookups/cage.query.xml @@ -9,6 +9,11 @@ Room + + ehr_lookups + rooms + room + true diff --git a/nbri_ehr/resources/queries/ehr_lookups/rooms.js b/nbri_ehr/resources/queries/ehr_lookups/rooms.js index caea28b..18a10a2 100644 --- a/nbri_ehr/resources/queries/ehr_lookups/rooms.js +++ b/nbri_ehr/resources/queries/ehr_lookups/rooms.js @@ -8,6 +8,19 @@ var console = require("console"); var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); +// Width of ehr_lookups.rooms.room. The derived key is built from values the user supplies, so it can overrun the +// column; reject it here rather than letting the database raise an unreadable error. +var MAX_ROOM_LENGTH = 100; + +// 'room' is not user editable, so it is absent from the incoming row map and the value this script derives has +// nowhere to land. Declaring it managed reserves a slot so the derived key is persisted. +function managedColumns() { + return { + insert: ["room"], + update: ["room"], + }; +} + function onUpsert(row, oldRow, errors){ if (extraContext.dataSource != "etl") { if (!row.name) { @@ -15,8 +28,8 @@ function onUpsert(row, oldRow, errors){ return; } - if (!row.floor) { - errors['floor'] = 'Floor is required.'; + if (!row.building) { + errors['building'] = 'Building is required.'; return; } @@ -26,7 +39,13 @@ function onUpsert(row, oldRow, errors){ return; } - row.room = row.name + '-' + row.floor; + let room = row.building + '-' + row.name; + if (room.length > MAX_ROOM_LENGTH) { + errors['name'] = 'Building and room name are too long: they combine to a ' + room.length + ' character room key, which cannot exceed ' + MAX_ROOM_LENGTH + '.'; + return; + } + + row.room = room; } } } diff --git a/nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml b/nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml index dd7b89f..0b522c5 100644 --- a/nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml +++ b/nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml @@ -6,8 +6,10 @@ Rooms - + + + /nbri_ehr/cageDetails.view?room=${room} true false false @@ -17,6 +19,14 @@ false false + + + true + false + false + false + diff --git a/nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml b/nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml index 0bfbf5b..f8c6e5e 100644 --- a/nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml +++ b/nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml index 5c829e1..e282d4d 100644 --- a/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml @@ -96,7 +96,7 @@ ehr_lookups rooms room - name + room diff --git a/nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml b/nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml index 4e381e4..243ffad 100644 --- a/nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml +++ b/nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml b/nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml index c3ca1ea..86bc194 100644 --- a/nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml +++ b/nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml index b08797c..6026d97 100644 --- a/nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml index b08797c..6026d97 100644 --- a/nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/alopecia/.qview.xml b/nbri_ehr/resources/queries/study/alopecia/.qview.xml index f889f92..b514468 100644 --- a/nbri_ehr/resources/queries/study/alopecia/.qview.xml +++ b/nbri_ehr/resources/queries/study/alopecia/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/behaviorCases/.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/.qview.xml index b08797c..6026d97 100644 --- a/nbri_ehr/resources/queries/study/behaviorCases/.qview.xml +++ b/nbri_ehr/resources/queries/study/behaviorCases/.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml index a48d5a5..5a68b93 100644 --- a/nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml +++ b/nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/blood/.qview.xml b/nbri_ehr/resources/queries/study/blood/.qview.xml index 831d6b5..c382d83 100644 --- a/nbri_ehr/resources/queries/study/blood/.qview.xml +++ b/nbri_ehr/resources/queries/study/blood/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/breeder/.qview.xml b/nbri_ehr/resources/queries/study/breeder/.qview.xml index 448bd0f..bba85e1 100644 --- a/nbri_ehr/resources/queries/study/breeder/.qview.xml +++ b/nbri_ehr/resources/queries/study/breeder/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/cases/.qview.xml b/nbri_ehr/resources/queries/study/cases/.qview.xml index 340d770..a2f1fbc 100644 --- a/nbri_ehr/resources/queries/study/cases/.qview.xml +++ b/nbri_ehr/resources/queries/study/cases/.qview.xml @@ -3,7 +3,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml index 8333562..7f83fe9 100644 --- a/nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml +++ b/nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml index 6081418..7554046 100644 --- a/nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml +++ b/nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml index 261b1bb..25baf96 100644 --- a/nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml +++ b/nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml index 73fb0b2..e0dd66f 100644 --- a/nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml +++ b/nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/chemistryResults/.qview.xml b/nbri_ehr/resources/queries/study/chemistryResults/.qview.xml index 02467cb..3cc536b 100644 --- a/nbri_ehr/resources/queries/study/chemistryResults/.qview.xml +++ b/nbri_ehr/resources/queries/study/chemistryResults/.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinicalCases/.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/.qview.xml index b08797c..6026d97 100644 --- a/nbri_ehr/resources/queries/study/clinicalCases/.qview.xml +++ b/nbri_ehr/resources/queries/study/clinicalCases/.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml index 7b1fc1a..0fe5c32 100644 --- a/nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml +++ b/nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinical_observations/.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/.qview.xml index daaa82d..8d99f0c 100644 --- a/nbri_ehr/resources/queries/study/clinical_observations/.qview.xml +++ b/nbri_ehr/resources/queries/study/clinical_observations/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml index 0a05b82..589eba9 100644 --- a/nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml +++ b/nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml index f7566f3..6c017a8 100644 --- a/nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml +++ b/nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml index adf8cf8..e8cff6b 100644 --- a/nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml +++ b/nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml index a48d5a5..5a68b93 100644 --- a/nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinremarks/.qview.xml b/nbri_ehr/resources/queries/study/clinremarks/.qview.xml index 903f88d..d96725e 100644 --- a/nbri_ehr/resources/queries/study/clinremarks/.qview.xml +++ b/nbri_ehr/resources/queries/study/clinremarks/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml b/nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml index 24f5a40..007434b 100644 --- a/nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml +++ b/nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml b/nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml index 6cb3771..3123f8c 100644 --- a/nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml +++ b/nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/demographics/.qview.xml b/nbri_ehr/resources/queries/study/demographics/.qview.xml index 439cd0a..d232062 100644 --- a/nbri_ehr/resources/queries/study/demographics/.qview.xml +++ b/nbri_ehr/resources/queries/study/demographics/.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/demographicsCagemates.sql b/nbri_ehr/resources/queries/study/demographicsCagemates.sql index b3464b7..4219925 100644 --- a/nbri_ehr/resources/queries/study/demographicsCagemates.sql +++ b/nbri_ehr/resources/queries/study/demographicsCagemates.sql @@ -22,10 +22,15 @@ SELECT FROM study.housing h JOIN study.housing h2 -ON (h2.Id.demographics.calculated_status = 'Alive' - AND (h.cage = h2.cage)) +-- cage holds a location key that already encodes the room, so caged animals match on cage alone. Group/pen rooms have +-- no cage, so those fall back to the room, which is only consulted when neither side has a cage. +ON ((h.cage = h2.cage OR (h.cage IS NULL AND h2.cage IS NULL AND h.room = h2.room)) + AND h2.Id.demographics.calculated_status = 'Alive' + AND h2.enddateTimeCoalesced >= now() + AND h2.qcstate.publicdata = true) WHERE h.enddateTimeCoalesced >= now() +AND h.qcstate.publicdata = true GROUP BY h.id, h.room, h.cage ) t ON (t.id = d.id) diff --git a/nbri_ehr/resources/queries/study/drug/.qview.xml b/nbri_ehr/resources/queries/study/drug/.qview.xml index 3b72268..8489e4d 100644 --- a/nbri_ehr/resources/queries/study/drug/.qview.xml +++ b/nbri_ehr/resources/queries/study/drug/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/drug/Behavior.qview.xml b/nbri_ehr/resources/queries/study/drug/Behavior.qview.xml index a9769cb..1688ad3 100644 --- a/nbri_ehr/resources/queries/study/drug/Behavior.qview.xml +++ b/nbri_ehr/resources/queries/study/drug/Behavior.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/exemptions/.qview.xml b/nbri_ehr/resources/queries/study/exemptions/.qview.xml index 7e4278b..cdd0721 100644 --- a/nbri_ehr/resources/queries/study/exemptions/.qview.xml +++ b/nbri_ehr/resources/queries/study/exemptions/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/flags/.qview.xml b/nbri_ehr/resources/queries/study/flags/.qview.xml index bf12e57..05657ca 100644 --- a/nbri_ehr/resources/queries/study/flags/.qview.xml +++ b/nbri_ehr/resources/queries/study/flags/.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/historicalOther.query.xml b/nbri_ehr/resources/queries/study/historicalOther.query.xml deleted file mode 100644 index 37e2754..0000000 --- a/nbri_ehr/resources/queries/study/historicalOther.query.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - Type - - -
- - - \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/housing.query.xml b/nbri_ehr/resources/queries/study/housing.query.xml index eeb5e0d..b08ae42 100644 --- a/nbri_ehr/resources/queries/study/housing.query.xml +++ b/nbri_ehr/resources/queries/study/housing.query.xml @@ -21,7 +21,6 @@ ehr_lookups cage location - cage @@ -31,7 +30,7 @@ ehr_lookups rooms room - name + room diff --git a/nbri_ehr/resources/queries/study/housing/.qview.xml b/nbri_ehr/resources/queries/study/housing/.qview.xml index bc780a5..5f01093 100644 --- a/nbri_ehr/resources/queries/study/housing/.qview.xml +++ b/nbri_ehr/resources/queries/study/housing/.qview.xml @@ -7,7 +7,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml b/nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml index 4fc3eeb..54e07b9 100644 --- a/nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml +++ b/nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml @@ -4,6 +4,7 @@ + diff --git a/nbri_ehr/resources/queries/study/notes/.qview.xml b/nbri_ehr/resources/queries/study/notes/.qview.xml index 6cd9bab..0f3a556 100644 --- a/nbri_ehr/resources/queries/study/notes/.qview.xml +++ b/nbri_ehr/resources/queries/study/notes/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/observationSchedule/.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/.qview.xml index b91d5d4..628bcd9 100644 --- a/nbri_ehr/resources/queries/study/observationSchedule/.qview.xml +++ b/nbri_ehr/resources/queries/study/observationSchedule/.qview.xml @@ -3,7 +3,7 @@ - + @@ -11,7 +11,7 @@ - + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order/.qview.xml b/nbri_ehr/resources/queries/study/observation_order/.qview.xml index c02d2fb..40bb429 100644 --- a/nbri_ehr/resources/queries/study/observation_order/.qview.xml +++ b/nbri_ehr/resources/queries/study/observation_order/.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml index d4c5c11..c2c3d7e 100644 --- a/nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml +++ b/nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml index 1638c87..f8bc797 100644 --- a/nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml +++ b/nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml index 343d9b8..ad56df0 100644 --- a/nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml +++ b/nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml index 5e1e749..24a0828 100644 --- a/nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml +++ b/nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/pairingSummary/.qview.xml b/nbri_ehr/resources/queries/study/pairingSummary/.qview.xml index f0fdcf4..48d82d6 100644 --- a/nbri_ehr/resources/queries/study/pairingSummary/.qview.xml +++ b/nbri_ehr/resources/queries/study/pairingSummary/.qview.xml @@ -6,7 +6,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml b/nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml index 14e0dfe..689f99f 100644 --- a/nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml +++ b/nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml @@ -9,7 +9,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml b/nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml index 1a11617..81ee864 100644 --- a/nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml +++ b/nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/pairings/.qview.xml b/nbri_ehr/resources/queries/study/pairings/.qview.xml index 26a8731..1a55dfa 100644 --- a/nbri_ehr/resources/queries/study/pairings/.qview.xml +++ b/nbri_ehr/resources/queries/study/pairings/.qview.xml @@ -6,7 +6,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/physicalExam/.qview.xml b/nbri_ehr/resources/queries/study/physicalExam/.qview.xml index caf3fb0..3fb7d6a 100644 --- a/nbri_ehr/resources/queries/study/physicalExam/.qview.xml +++ b/nbri_ehr/resources/queries/study/physicalExam/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/prc/.qview.xml b/nbri_ehr/resources/queries/study/prc/.qview.xml index f5ed643..089bd36 100644 --- a/nbri_ehr/resources/queries/study/prc/.qview.xml +++ b/nbri_ehr/resources/queries/study/prc/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/prcOverdue/.qview.xml b/nbri_ehr/resources/queries/study/prcOverdue/.qview.xml index b8bf120..7957d9f 100644 --- a/nbri_ehr/resources/queries/study/prcOverdue/.qview.xml +++ b/nbri_ehr/resources/queries/study/prcOverdue/.qview.xml @@ -3,7 +3,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/prcSchedule/.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/.qview.xml index 4604b77..227ae69 100644 --- a/nbri_ehr/resources/queries/study/prcSchedule/.qview.xml +++ b/nbri_ehr/resources/queries/study/prcSchedule/.qview.xml @@ -3,7 +3,7 @@ - + @@ -17,7 +17,7 @@ - + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc_order/.qview.xml b/nbri_ehr/resources/queries/study/prc_order/.qview.xml index b9de6c1..8da38d4 100644 --- a/nbri_ehr/resources/queries/study/prc_order/.qview.xml +++ b/nbri_ehr/resources/queries/study/prc_order/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/prc_order_report/.qview.xml b/nbri_ehr/resources/queries/study/prc_order_report/.qview.xml index 62d20f0..3402400 100644 --- a/nbri_ehr/resources/queries/study/prc_order_report/.qview.xml +++ b/nbri_ehr/resources/queries/study/prc_order_report/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml index 4c57f0b..e773c14 100644 --- a/nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml @@ -3,7 +3,7 @@ - + @@ -22,7 +22,7 @@ - + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatment_order/.qview.xml b/nbri_ehr/resources/queries/study/treatment_order/.qview.xml index 27608af..2b14b7b 100644 --- a/nbri_ehr/resources/queries/study/treatment_order/.qview.xml +++ b/nbri_ehr/resources/queries/study/treatment_order/.qview.xml @@ -2,7 +2,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/vitals/.qview.xml b/nbri_ehr/resources/queries/study/vitals/.qview.xml index f3b831c..b6bc349 100644 --- a/nbri_ehr/resources/queries/study/vitals/.qview.xml +++ b/nbri_ehr/resources/queries/study/vitals/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/queries/study/weight/.qview.xml b/nbri_ehr/resources/queries/study/weight/.qview.xml index b27ffe4..b6d1a95 100644 --- a/nbri_ehr/resources/queries/study/weight/.qview.xml +++ b/nbri_ehr/resources/queries/study/weight/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml index 1d03f01..a4cd2a4 100644 --- a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml +++ b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml @@ -20,7 +20,6 @@ - diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml index 42317f7..47283a3 100644 --- a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -623,30 +623,6 @@ - - - - varchar - http://cpas.labkey.com/Study#ParticipantId - - ptid - - - - timestamp - http://cpas.labkey.com/Study#VisitDate - http://cpas.labkey.com/Study#VisitDate - - - varchar - - - varchar - - - Historical Other - Captures miscellaneous historical health and research records for primates that do not fit other specific categories. -
HousingTracks housing assignments and location transfers for primates within the research facility. diff --git a/nbri_ehr/resources/reports/additionalReports.tsv b/nbri_ehr/resources/reports/additionalReports.tsv index 8eddd91..efaa2ad 100644 --- a/nbri_ehr/resources/reports/additionalReports.tsv +++ b/nbri_ehr/resources/reports/additionalReports.tsv @@ -49,5 +49,4 @@ behaviorRemarks Behavior query Behavior Remarks true study BehaviorClinRemarks clinObsBehavior Behavior query Observations true study behaviorObservations date false false qcstate/publicdata This report contains one record for each encounter with each animal, including surergies, exams, procedures, etc. clinremarks Clinical query Clinical Remarks true study ClinicalClinRemarks date false false qcstate/publicdata This report contains the clinical remarks entered about each animal physicalExam Clinical query Exam History True study physicalExam date false false qcstate/publicdata This report displays physical exam data for the selected animal -historicalOther General query Historical True study historicalOther date false false qcstate/publicdata This report displays historical events from legacy systems conceptionsByDam Reproductive Management query Conceptions by Dam true nbri_ehr ConceptionsByDam ConceptDate false false qcstate/publicdata This report displays conception records where the selected animal is the dam \ No newline at end of file diff --git a/nbri_ehr/resources/views/cageDetails.html b/nbri_ehr/resources/views/cageDetails.html index a0c5da2..fde98de 100644 --- a/nbri_ehr/resources/views/cageDetails.html +++ b/nbri_ehr/resources/views/cageDetails.html @@ -42,7 +42,7 @@ schemaName: 'ehr_lookups', queryName: 'cage', filterArray: detailFilterArray, - columns: 'cage,room,room/floor,room/floor/building,room/floor/building/area,outdoor', + columns: 'cage,room,room/building,room/building/area,outdoor', }, title: 'Cage Details', renderTo: 'cageDetails_' + webpart.wrapperDivId, @@ -56,7 +56,7 @@ queryName: 'cage', filterArray: detailFilterArray, sort: 'cage', - columns: 'cage,room,room/floor,room/floor/building,room/floor/building/area,outdoor', + columns: 'cage,room,room/building,room/building/area,outdoor', }).render('cageDetails_' + webpart.wrapperDivId); } diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIHousingDataSource.java b/nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIHousingDataSource.java index 91fdf41..0749f01 100644 --- a/nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIHousingDataSource.java +++ b/nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIHousingDataSource.java @@ -36,7 +36,7 @@ public NBRIHousingDataSource(Module module) @Override protected Set getColumnNames() { - return PageFlowUtil.set("Id", "date", "cage/cage", "room/fullRoom", "reason", "remark"); + return PageFlowUtil.set("Id", "date", "cage/cage", "room/room", "reason", "remark"); } @Override @@ -44,7 +44,7 @@ protected String getHtml(Container c, Results rs, boolean redacted) throws SQLEx { StringBuilder sb = new StringBuilder(); - FieldKey room = FieldKey.fromString("room/fullRoom"); + FieldKey room = FieldKey.fromString("room/room"); FieldKey cage = FieldKey.fromString("cage/cage"); String value = "Unknown"; if (rs.hasColumn(cage) && rs.getObject(cage) != null) diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java b/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java index 38fd24d..b365680 100644 --- a/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java +++ b/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java @@ -93,16 +93,6 @@ public void customize(TableInfo table) customizeTasks(ti); } - if (matches(ti, "ehr_lookups", "rooms")) - { - customizeRooms(ti); - } - - if (matches(ti, "ehr_lookups", "floors")) - { - customizeFloors(ti); - } - if (matches(ti, "nbri_ehr", "necropsyTasks")) { addNecropsyReportLink(ti); @@ -581,60 +571,6 @@ public boolean isEditable() } } - private void customizeRooms(AbstractTableInfo ti) - { - ColumnInfo roomCol = ti.getColumn("name"); - ColumnInfo floorCol = ti.getColumn("floor"); - if (roomCol != null && floorCol != null && ti.getColumn("fullRoom") == null) - { - ExprColumn col = new ExprColumn(ti, new FieldKey(null, "fullRoom"), new SQLFragment("##ERROR"), JdbcType.VARCHAR, roomCol, floorCol) { - @Override - public SQLFragment getValueSql(String tableAlias) - { - // Need to subclass and override this function due to issue using ExprColumn.STR_TABLE_ALIAS with extensible columns - SQLFragment sql = new SQLFragment("(SELECT COALESCE(r.room, 'Room N/A') || ', ' || COALESCE(r.floor, 'Floor N/A') || ', ' || COALESCE(r.building, 'Building N/A') \n" + - " FROM (\n" + - " SELECT \n").append(roomCol.getValueSql(tableAlias)); - sql.append(" AS room,\n" + - " ff.name as floor,\n" + - " bb.description as building\n" + - " FROM ehr_lookups.floors ff \n" + - " JOIN ehr_lookups.buildings bb ON ff.building = bb.name\n" + - " WHERE ff.floor =\n").append(floorCol.getValueSql(tableAlias)); - sql.append(" ) r\n" + - " )"); - - return sql; - } - }; - col.setName("fullRoom"); - col.setLabel("Full Room"); - ti.addColumn(col); - } - } - - private void customizeFloors(AbstractTableInfo ti) - { - ColumnInfo floorCol = ti.getColumn("name"); - ColumnInfo bldgCol = ti.getColumn("building"); - if (floorCol != null && bldgCol != null && ti.getColumn("fullFloor") == null) - { - SQLFragment sql = new SQLFragment("(SELECT COALESCE(r.floor, 'Floor N/A') || ', ' || COALESCE(r.building, 'Building N/A') \n" + - " FROM (\n" + - " SELECT " + ExprColumn.STR_TABLE_ALIAS + ".name\n"); - sql.append(" AS floor,\n" + - " bb.description as building\n" + - " FROM ehr_lookups.buildings bb \n" + - " WHERE bb.name = " + ExprColumn.STR_TABLE_ALIAS + ".building\n"); - sql.append(" ) r\n" + - " )"); - - ExprColumn col = new ExprColumn(ti, "fullFloor", sql, JdbcType.VARCHAR, floorCol, bldgCol); - col.setLabel("Full Floor"); - ti.addColumn(col); - } - } - private void customizeTasks(AbstractTableInfo ti) { DetailsURL detailsURL = DetailsURL.fromString("/ehr/dataEntryFormDetails.view?formType=${formtype}&taskid=${taskid}"); @@ -777,7 +713,7 @@ public void doSharedCustomization(AbstractTableInfo ti) { UserSchema us = getEHRUserSchema(ti, "ehr_lookups"); col.setLabel("Room"); - col.setFk(new QueryForeignKey(ti.getUserSchema(), ti.getContainerFilter(), us, null, "rooms", "room", "fullRoom")); + col.setFk(new QueryForeignKey(ti.getUserSchema(), ti.getContainerFilter(), us, null, "rooms", "room", "room")); col.setURL(StringExpressionFactory.createURL("/nbri_ehr/cageDetails.view?room=${room}")); } if ("building".equalsIgnoreCase(col.getName()) && !ti.getName().equalsIgnoreCase("buildings")) @@ -790,7 +726,7 @@ public void doSharedCustomization(AbstractTableInfo ti) { UserSchema us = getEHRUserSchema(ti, "ehr_lookups"); col.setLabel("Floor"); - col.setFk(new QueryForeignKey(ti.getUserSchema(), ti.getContainerFilter(), us, null, "floors", "floor", "fullFloor")); + col.setFk(new QueryForeignKey(ti.getUserSchema(), ti.getContainerFilter(), us, null, "floors", "floor", "name")); } if ("area".equalsIgnoreCase(col.getName()) && !ti.getName().equalsIgnoreCase("areas")) { diff --git a/nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetHousing.tsv b/nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetHousing.tsv index 23969c0..487f797 100644 --- a/nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetHousing.tsv +++ b/nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetHousing.tsv @@ -1,9 +1,9 @@ -objectid Id QCStateLabel date enddate cage performedby -1 44444 Completed -1381d -1321d 11 - Rm 202B - ZZA 1004 -2 44444 Completed -1321d 11 - Rm 202B - ZZB 1004 -3 44446 Completed -1406d -1316d 11 - Rm 202B - ZZA 1004 -4 44446 Completed -1316d 11 - Rm 202B - ZZC 1004 -5 TEST4551032 Completed -6362d 11 - Rm 202B - ZZD 1004 -6 44442 Completed -6100d -5920d 11 - Rm 202B - ZZA 1004 -7 44442 Completed -5920d 11 - Rm 202B - ZZC 1004 -8 44443 Completed -6100d 11 - Rm 202B - ZZF 1004 +objectid Id QCStateLabel date enddate room cage performedby +1 44444 Completed -1381d -1321d TestBuilding-R1 TestBuilding-R1-C1 1004 +2 44444 Completed -1321d TestBuilding-R1 TestBuilding-R1-C2 1004 +3 44446 Completed -1406d -1316d TestBuilding-R1 TestBuilding-R1-C1 1004 +4 44446 Completed -1316d TestBuilding-R2 TestBuilding-R2-C3 1004 +5 TEST4551032 Completed -6362d TestBuilding-R3 TestBuilding-R3-C4 1004 +6 44442 Completed -6100d -5920d TestBuilding-R1 TestBuilding-R1-C1 1004 +7 44442 Completed -5920d TestBuilding-R2 TestBuilding-R2-C3 1004 +8 44443 Completed -6100d TestBuilding-R1 TestBuilding-R1-C2 1004 diff --git a/nbri_ehr/test/src/org.labkey.test/tests.nbri_ehr/NBRI_EHRTest.java b/nbri_ehr/test/src/org.labkey.test/tests.nbri_ehr/NBRI_EHRTest.java index a06c389..487d1f2 100644 --- a/nbri_ehr/test/src/org.labkey.test/tests.nbri_ehr/NBRI_EHRTest.java +++ b/nbri_ehr/test/src/org.labkey.test/tests.nbri_ehr/NBRI_EHRTest.java @@ -34,6 +34,8 @@ import org.labkey.remoteapi.query.ImportDataCommand; import org.labkey.remoteapi.query.InsertRowsCommand; import org.labkey.remoteapi.query.RowsResponse; +import org.labkey.remoteapi.query.SelectRowsCommand; +import org.labkey.remoteapi.query.SelectRowsResponse; import org.labkey.remoteapi.security.CreateUserResponse; import org.labkey.test.Locator; import org.labkey.test.TestFileUtils; @@ -107,6 +109,28 @@ public class NBRI_EHRTest extends AbstractGenericEHRTest implements PostgresOnly // createTestSubjects so the clinical case form raises no warnings that would keep the validation banner up. private static final String taskGroupAnimalId = "TESTGRP9090"; + // Rooms are keyed by building and name, so every room fixture needs a building to hang off of. + // 'buildings' derives its key from the description, and 'SPF' is one of the areas seeded with the ehr_lookups schema. + private static final String BUILDING_ID = "TestBuilding"; + private static final String BUILDING_AREA = "SPF"; + + // Cage locations seeded by populateLocations, named for the room each one sits in. The cage trigger derives these + // from the room and cage, and housing records key off the location, so these are what belongs in a housing row's + // 'cage' field. datasetHousing.tsv spells the same values out, since a TSV cannot call cageLocation. + private static final String CAGE_IN_R1 = cageLocation("R1", "C1"); + private static final String CAGE_IN_R3 = cageLocation("R3", "C4"); + + // A group pen has no cage, so its location is the room key alone. Created by testGroupPenCagemates. + private static final String PEN_ROOM_NAME = "PEN1"; + private static final String[] PEN_ANIMALS = {"PEN0001", "PEN0002"}; + + // Housed with a cage but no room, which is how a record entered against a cage alone lands. Every cage seeded by + // populateLocations already has occupants from datasetHousing.tsv, so testCagematesWithoutRoom creates its own to + // keep the expected cagemate count exact. + private static final String ROOMLESS_CAGE_NAME = "C9"; + private static final String ROOMLESS_CAGE = cageLocation("R1", ROOMLESS_CAGE_NAME); + private static final String[] ROOMLESS_ANIMALS = {"CAGE0001", "CAGE0002"}; + private final String[] weightFields = {"Id", "date", "enddate", "project", "weight", FIELD_QCSTATELABEL, FIELD_OBJECTID, FIELD_LSID, "_recordid", "performedby"}; private final Object[] weightData1 = {getExpectedAnimalIDCasing("TESTSUBJECT1"), EHRClientAPIHelper.DATE_SUBSTITUTION, null, null, "12", EHRQCState.IN_PROGRESS.label, null, null, "_recordID", 1004}; @@ -244,20 +268,62 @@ private void populateFormulary() throws IOException, CommandException RowsResponse saveRowsResponse = insertRowsCommand.execute(getApiHelper().getConnection(), getContainerPath()); } + /** + * The key a room trigger derives for the given room name. Mirrors ehr_lookups/rooms.js. + */ + private static String roomKey(String roomName) + { + return BUILDING_ID + "-" + roomName; + } + + /** + * The location a cage trigger derives for the given room and cage. Mirrors ehr_lookups/cage.js. + */ + private static String cageLocation(String roomName, String cageName) + { + return roomKey(roomName) + "-" + cageName; + } + + /** + * Housing records store the derived room key, so the fixture rooms have to be named by key for the room + * lookups to resolve. The base implementation returns names that match no room in this study. + */ + @Override + protected String[] getRooms() + { + return new String[]{roomKey("R1"), roomKey("R2"), roomKey("R3")}; + } + + @LogMethod + private void populateBuildingRecords() throws Exception + { + InsertRowsCommand insertCmd = new InsertRowsCommand("ehr_lookups", "buildings"); + Map rowMap = new HashMap<>(); + // Supply the derived key rather than relying on the trigger to fill it, matching how the base class seeds rooms. + rowMap.put("name", BUILDING_ID); + rowMap.put("description", BUILDING_ID); + rowMap.put("area", BUILDING_AREA); + insertCmd.addRow(rowMap); + + insertCmd.execute(createDefaultConnection(), getContainerPath()); + } + @Override protected void populateRoomRecords() throws Exception { + populateBuildingRecords(); + InsertRowsCommand insertCmd = new InsertRowsCommand("ehr_lookups", "rooms"); Map rowMap = new HashMap<>(); rowMap.put("name", ROOM_ID); - rowMap.put("floor", "floor1"); + rowMap.put("building", BUILDING_ID); rowMap.put("housingType", 1); rowMap.put("housingCondition", 1); insertCmd.addRow(rowMap); rowMap = new HashMap<>(); rowMap.put("name", ROOM_ID2); - rowMap.put("floor", "floor2"); + rowMap.put("building", BUILDING_ID); rowMap.put("housingType", 1); rowMap.put("housingCondition", 1); insertCmd.addRow(rowMap); @@ -321,19 +387,21 @@ private void enableNotification(String notification) private void populateLocations() throws IOException, CommandException { goToEHRFolder(); + // BUILDING_ID is created by populateRoomRecords, which runs earlier as part of initProject. log("Inserting values in rooms"); InsertRowsCommand roomCmd = new InsertRowsCommand("ehr_lookups", "rooms"); - roomCmd.addRow(Map.of("name", "R1", "floor", "F1")); - roomCmd.addRow(Map.of("name", "R2", "floor", "F2")); - roomCmd.addRow(Map.of("name", "R3", "floor", "F3")); + roomCmd.addRow(Map.of("name", "R1", "building", BUILDING_ID)); + roomCmd.addRow(Map.of("name", "R2", "building", BUILDING_ID)); + roomCmd.addRow(Map.of("name", "R3", "building", BUILDING_ID)); roomCmd.execute(getApiHelper().getConnection(), getContainerPath()); + // 'location' is left out so the cage trigger derives it, exercising the same path production entry takes. log("Inserting values in cage"); InsertRowsCommand cageCmd = new InsertRowsCommand("ehr_lookups", "cage"); - cageCmd.addRow(Map.of("location", "L1", "cage", "C1", "room", "R1")); - cageCmd.addRow(Map.of("location", "L2", "cage", "C2", "room", "R1")); - cageCmd.addRow(Map.of("location", "L3", "cage", "C3", "room", "R2")); - cageCmd.addRow(Map.of("location", "L4", "cage", "C4", "room", "R3")); + cageCmd.addRow(Map.of("cage", "C1", "room", roomKey("R1"))); + cageCmd.addRow(Map.of("cage", "C2", "room", roomKey("R1"))); + cageCmd.addRow(Map.of("cage", "C3", "room", roomKey("R2"))); + cageCmd.addRow(Map.of("cage", "C4", "room", roomKey("R3"))); cageCmd.execute(getApiHelper().getConnection(), getContainerPath()); } @@ -439,10 +507,10 @@ protected void createTestSubjects() throws Exception log("Creating initial housing records"); fields = new String[]{"Id", "date", "enddate", "room", "cage", "performedby"}; data = new Object[][]{ - {SUBJECTS[0], pastDate1, pastDate2, getRooms()[0], CAGES[0], 1004}, - {SUBJECTS[0], pastDate2, null, getRooms()[0], CAGES[0], 1004}, - {SUBJECTS[1], pastDate1, pastDate2, getRooms()[0], CAGES[0], 1004}, - {SUBJECTS[1], pastDate2, null, getRooms()[2], CAGES[2], 1004} + {SUBJECTS[0], pastDate1, pastDate2, getRooms()[0], CAGE_IN_R1, 1004}, + {SUBJECTS[0], pastDate2, null, getRooms()[0], CAGE_IN_R1, 1004}, + {SUBJECTS[1], pastDate1, pastDate2, getRooms()[0], CAGE_IN_R1, 1004}, + {SUBJECTS[1], pastDate2, null, getRooms()[2], CAGE_IN_R3, 1004} }; insertCommand = getApiHelper().prepareInsertCommand("study", "Housing", "lsid", fields, data); getApiHelper().deleteAllRecords("study", "Housing", new Filter("Id", StringUtils.join(SUBJECTS, ";"), Filter.Operator.IN)); @@ -486,7 +554,7 @@ protected void createTestSubjects() throws Exception fields = new String[]{"Id", "date", "enddate", "room", "cage", "performedby"}; data = new Object[][]{ - {taskGroupAnimalId, pastDate1, null, getRooms()[0], CAGES[0], 1004} + {taskGroupAnimalId, pastDate1, null, getRooms()[0], CAGE_IN_R1, 1004} }; insertCommand = getApiHelper().prepareInsertCommand("study", "Housing", "lsid", fields, data); getApiHelper().deleteAllRecords("study", "Housing", new Filter("Id", taskGroupAnimalId)); @@ -1233,7 +1301,7 @@ public void createSubjectsForDeathForm() throws IOException, CommandException project.execute(getApiHelper().getConnection(), getContainerPath()); InsertRowsCommand housing = new InsertRowsCommand("study", "housing"); - housing.addRow(Map.of("Id", aliveAnimalId, "date", LocalDateTime.now().minusDays(10), "cage", "C4", "QCStateLabel", "Completed", "performedby", 1004)); + housing.addRow(Map.of("Id", aliveAnimalId, "date", LocalDateTime.now().minusDays(10), "room", getRooms()[2], "cage", CAGE_IN_R3, "QCStateLabel", "Completed", "performedby", 1004)); housing.execute(getApiHelper().getConnection(), getContainerPath()); log("Marking an animal dead"); @@ -1536,6 +1604,159 @@ public void testCalculatedAgeColumns() assertEquals("Calculated ages are incorrect", Arrays.asList("4.8", "4.0", "58.0"), row.subList(columnCount - 3, columnCount)); } + @Test + public void testRoomKeyDerivation() throws Exception + { + log("Verifying a room derives its key from its building and name"); + SelectRowsCommand selectCmd = new SelectRowsCommand("ehr_lookups", "rooms"); + selectCmd.setColumns(List.of("room", "name", "building")); + selectCmd.addFilter(new Filter("name", "R1")); + SelectRowsResponse response = selectCmd.execute(getApiHelper().getConnection(), getContainerPath()); + + Assert.assertEquals("Expected exactly one room named R1", 1, response.getRows().size()); + Map room = response.getRows().get(0); + Assert.assertEquals("Room key should combine the building and the name", roomKey("R1"), room.get("room")); + Assert.assertEquals("Room should belong to the seeded building", BUILDING_ID, room.get("building")); + } + + @Test + public void testRoomRequiresBuilding() + { + log("Verifying a room cannot be created without a building"); + InsertRowsCommand insertCmd = new InsertRowsCommand("ehr_lookups", "rooms"); + insertCmd.addRow(Map.of("name", "NOBUILDING")); + + try + { + insertCmd.execute(getApiHelper().getConnection(), getContainerPath()); + Assert.fail("Room insert should have been rejected when no building was supplied"); + } + catch (IOException | CommandException e) + { + Assert.assertTrue("Unexpected failure inserting a room without a building: " + e.getMessage(), + e.getMessage() != null && e.getMessage().contains("Building is required")); + } + } + + @Test + public void testDuplicateBuildingRejected() + { + log("Verifying a second building cannot reuse an existing description"); + // The description alone is the building key now, so reusing the seeded building's description would collide. + InsertRowsCommand insertCmd = new InsertRowsCommand("ehr_lookups", "buildings"); + insertCmd.addRow(Map.of("description", BUILDING_ID, "area", BUILDING_AREA)); + + try + { + insertCmd.execute(getApiHelper().getConnection(), getContainerPath()); + Assert.fail("Building insert should have been rejected when the description was already in use"); + } + catch (IOException | CommandException e) + { + Assert.assertTrue("Unexpected failure inserting a duplicate building: " + e.getMessage(), + e.getMessage() != null && e.getMessage().contains("already exists")); + } + } + + @Test + public void testGroupPenCagemates() throws Exception + { + String penRoom = roomKey(PEN_ROOM_NAME); + + log("Creating a group pen, whose location is the room with no cage"); + InsertRowsCommand roomCmd = new InsertRowsCommand("ehr_lookups", "rooms"); + roomCmd.addRow(Map.of("name", PEN_ROOM_NAME, "building", BUILDING_ID)); + roomCmd.execute(getApiHelper().getConnection(), getContainerPath()); + + // With no cage supplied the trigger derives the location as the room key alone. + InsertRowsCommand penCmd = new InsertRowsCommand("ehr_lookups", "cage"); + penCmd.addRow(Map.of("room", penRoom)); + penCmd.execute(getApiHelper().getConnection(), getContainerPath()); + + createAliveAnimals(PEN_ANIMALS); + + // The cage is deliberately left null: a penned animal is housed against the room, which is the case the + // cagemates query has to bound by room rather than by cage. + log("Housing two animals in the pen, with no cage"); + houseAnimals(PEN_ANIMALS, penRoom, null); + + log("Verifying penned animals resolve as each other's cagemates"); + assertCagemates(PEN_ANIMALS[0], 2, PEN_ANIMALS[1]); + } + + @Test + public void testCagematesWithoutRoom() throws Exception + { + log("Creating an unoccupied cage"); + InsertRowsCommand cageCmd = new InsertRowsCommand("ehr_lookups", "cage"); + cageCmd.addRow(Map.of("cage", ROOMLESS_CAGE_NAME, "room", roomKey("R1"))); + cageCmd.execute(getApiHelper().getConnection(), getContainerPath()); + + createAliveAnimals(ROOMLESS_ANIMALS); + + // The cage is a location key that already names its room, so the room is redundant here and nothing requires + // it. Cagemates must still resolve when it is absent. + log("Housing two animals in the same cage, with no room"); + houseAnimals(ROOMLESS_ANIMALS, null, ROOMLESS_CAGE); + + log("Verifying caged animals resolve as each other's cagemates without a room"); + assertCagemates(ROOMLESS_ANIMALS[0], 2, ROOMLESS_ANIMALS[1]); + } + + /** + * Creates living demographics records for the given animals, replacing any left behind by an earlier run. + */ + private void createAliveAnimals(String[] animalIds) throws Exception + { + log("Creating animals " + StringUtils.join(animalIds, ", ")); + String[] fields = new String[]{"Id", "Species", "Birth", "Gender", "date", "calculated_status", "objectid", "performedby"}; + Object[][] data = new Object[animalIds.length][]; + for (int i = 0; i < animalIds.length; i++) + { + data[i] = new Object[]{animalIds[i], "Rhesus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}; + } + + SimplePostCommand insertCommand = getApiHelper().prepareInsertCommand("study", "demographics", "lsid", fields, data); + getApiHelper().deleteAllRecords("study", "demographics", new Filter("Id", StringUtils.join(animalIds, ";"), Filter.Operator.IN)); + getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), insertCommand, getExtraContext()); + } + + /** + * Opens a completed housing record for each animal at the given location, replacing any left behind by an earlier + * run. Either the room or the cage may be null, which is how records entered against one alone land. + */ + private void houseAnimals(String[] animalIds, String room, String cage) throws Exception + { + String[] fields = new String[]{"Id", "date", "enddate", "room", "cage", "QCStateLabel", "performedby"}; + Object[][] data = new Object[animalIds.length][]; + for (int i = 0; i < animalIds.length; i++) + { + data[i] = new Object[]{animalIds[i], new Date(), null, room, cage, EHRQCState.COMPLETED.label, 1004}; + } + + SimplePostCommand insertCommand = getApiHelper().prepareInsertCommand("study", "Housing", "lsid", fields, data); + getApiHelper().deleteAllRecords("study", "Housing", new Filter("Id", StringUtils.join(animalIds, ";"), Filter.Operator.IN)); + getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), insertCommand, getExtraContext()); + } + + /** + * Asserts the cagemates report resolves the expected companions for an animal. A null total means the join matched + * nothing at all, which is reported as its own failure rather than as an unexpected count. + */ + private void assertCagemates(String animalId, int expectedTotal, String expectedCompanion) throws Exception + { + SelectRowsCommand selectCmd = new SelectRowsCommand("study", "demographicsCagemates"); + selectCmd.addFilter(new Filter("Id", animalId)); + SelectRowsResponse response = selectCmd.execute(getApiHelper().getConnection(), getContainerPath()); + + Assert.assertEquals("Expected one cagemates row for " + animalId, 1, response.getRows().size()); + Map cagemates = response.getRows().get(0); + Assert.assertNotNull("Cagemates resolved no location for " + animalId, cagemates.get("total")); + Assert.assertEquals("Unexpected cagemate count for " + animalId, expectedTotal, ((Number) cagemates.get("total")).intValue()); + Assert.assertTrue("Cagemate list should name " + expectedCompanion + ", was: " + cagemates.get("animals"), + String.valueOf(cagemates.get("animals")).contains(expectedCompanion)); + } + @Test public void testLookupPage() throws Exception {