25.7 fb pairing observation enhancement revised

onprc_ehr/resources/data/lookup_sets.tsv

@@ -1,82 +1,85 @@
 setname	label	keyfield	titleColumn
-PregnancyConfirm	Pregnancy Confirmation Types	
-housingDefinition	Housing Definition	
-housingTypes	Housing Types	
-AcquistionType	Acquistion Types	value
-RearingType	Rearing Types	
-MatingType	Mating Types	
-pairingEventType	Pairing Event Types	value
-tb_method	TB Test Methods	value
-microbiologyQuantity	Microbiology Quantity	value
-blood_sample_type	Blood Sample Types	value
-pairingHousingType	Pairing Housing Types	value
-pairingOutcome	Pairing Outcomes	value
-pairingGoal	Pairing Goal	value
-pairingObservation	Pairing Observations	value
-antibioticSensitivityResult	Antibiotic Sensitivity Result	value
-pairingSeparationReason	Pairing Separation Reason	value
-tissue_preparation	Tissue Preparation	value
-tissue_condition	Tissue Condition	value
-drugReason	Drug Reason	value
-serologyMethod	Serology Methods	value
-TransferReason	Transfer Reasons	
-assignmentReleaseType	Assignment Release Types	value
-animalGroupReleaseType	Animal Group Release Types	value
-observation_areas	Observation Areas	value
-drugOutcome	Drug Administration Outcomes	value
-encounterSummaryCategory	Encounter Summary Category	value
-labworkChargeType	Labwork Charge Types	value
-notes_category	DCM Notes Category	value
-blood_draw_reason	Blood Draw Reason	value
-encounter_roles	Encounter Roles	value
-parentageRelationship	Parentage Relationship	value
-parentageMethod	Parentage Determination Methods	value
-serologyResultQualifier	Serology Result Qualifier	value
-app_score	Appetite Score	value
-att_score	Attitude Score	value
-turgor_score	Turgor Score	value
-hyd_score	Hyd Score	value
-stool_score	Stool Score	value
-sib_score	SIB Score	value
-incision_score	Incision Score	value
-alopecia_type	Alopecia Type	value
-alopecia_score	Alopecia Type	value
-alopecia_regrowth	Alopecia Regrowth	value
-mens_score	Mens Score	value
-vomit	Vomit	value
-tissue_sample_type	Tissue Distribution Sample Type	value
-tissue_distribution_category	Tissue Distribution Request Category	value
-cage_status	Cage Status	value
-project_use_category	Center Project Use Categories	value
-project_type	Center Project Types	value
-procedure_drug_templates	Procedure Drug Templates	value
-behavior_types	Behavior Types	value
-fecal_smear_score	Fecal Smear Scores	value
-problem_list_subcategory	Problem List Subcategory	value
-customer_affiliation	Customer Affiliation	value
-birth_date_type	Birth Date Type	value
-birth_type	Birth Type Field Values	value
-chemistry_method	Chemistry Method Field Values	value
-clinpath_sampletype	Clinpath Sample Type Field Values	value
-clinpath_types	Clinpath Type Field Values	value
-clinremarks_category	Clinremarks Category Field Values	value
-drug_categories	Drug Category Field Values	value
-hematology_method	Hematology Method Field Values	value
-problem_list_category	Problem List Category Field Values	value
-parasitology_method	Parasitology Method Field Values	value
-urinalysis_method	Urinalysis Method Field Values	value
-urinalysis_qualitative_results	Urinalysis Qualitative Result Field Values	value
-bcs_score	BCS Score Field Values	value
-avail_codes Availability Code Field Values	value
-status_codes	Status Code Field Values	value
-snomed_qualifiers	SNOMED Code Qualifiers	value
-housing_reason	Housing Reason Field Values	value
-housing_condition_codes	Housing Condition Field Values	value
-histology_stain	Histology Stain Field Values	value
-encounter_types	Encounter Types	value
-DeliveryMode	Delivery Mode Field Values	value
-DeliveryType	Delivery Type Field Values	value
-death_manner	Death Manner	value
-death_cause	Death Cause	value
-ConfirmationType	Pregnancy Confirmation Type	value
-clinpath_collection_method	Clinpath Collection Method	value
+PregnancyConfirm	Pregnancy Confirmation Types		
+housingDefinition	Housing Definition		
+housingTypes	Housing Types		
+AcquistionType	Acquistion Types	value	
+RearingType	Rearing Types		
+MatingType	Mating Types		
+pairingEventType	Pairing Event Types	value	
+tb_method	TB Test Methods	value	
+microbiologyQuantity	Microbiology Quantity	value	
+blood_sample_type	Blood Sample Types	value	
+pairingHousingType	Pairing Housing Types	value	
+pairingpriorgroups	 Pairing Prior groups	value
+pairingendtypes	Pairing End Types	value	
+pairingstarttype	Pairing Start Type	value	
+pairingOutcome	Pairing Outcomes	value	
+pairingGoal	Pairing Goal	value	
+pairingObservation	Pairing Observations	value	
+antibioticSensitivityResult	Antibiotic Sensitivity Result	value	
+pairingSeparationReason	Pairing Separation Reason	value	
+tissue_preparation	Tissue Preparation	value	
+tissue_condition	Tissue Condition	value	
+drugReason	Drug Reason	value	
+serologyMethod	Serology Methods	value	
+TransferReason	Transfer Reasons		
+assignmentReleaseType	Assignment Release Types	value	
+animalGroupReleaseType	Animal Group Release Types	value	
+observation_areas	Observation Areas	value	
+drugOutcome	Drug Administration Outcomes	value	
+encounterSummaryCategory	Encounter Summary Category	value	
+labworkChargeType	Labwork Charge Types	value	
+notes_category	DCM Notes Category	value	
+blood_draw_reason	Blood Draw Reason	value	
+encounter_roles	Encounter Roles	value	
+parentageRelationship	Parentage Relationship	value	
+parentageMethod	Parentage Determination Methods	value	
+serologyResultQualifier	Serology Result Qualifier	value	
+app_score	Appetite Score	value	
+att_score	Attitude Score	value	
+turgor_score	Turgor Score	value	
+hyd_score	Hyd Score	value	
+stool_score	Stool Score	value	
+sib_score	SIB Score	value	
+incision_score	Incision Score	value	
+alopecia_type	Alopecia Type	value	
+alopecia_score	Alopecia Type	value	
+alopecia_regrowth	Alopecia Regrowth	value	
+mens_score	Mens Score	value	
+vomit	Vomit	value	
+tissue_sample_type	Tissue Distribution Sample Type	value	
+tissue_distribution_category	Tissue Distribution Request Category	value	
+cage_status	Cage Status	value	
+project_use_category	Center Project Use Categories	value	
+project_type	Center Project Types	value	
+procedure_drug_templates	Procedure Drug Templates	value	
+behavior_types	Behavior Types	value	
+fecal_smear_score	Fecal Smear Scores	value	
+problem_list_subcategory	Problem List Subcategory	value	
+customer_affiliation	Customer Affiliation	value	
+birth_date_type	Birth Date Type	value	
+birth_type	Birth Type Field Values	value	
+chemistry_method	Chemistry Method Field Values	value	
+clinpath_sampletype	Clinpath Sample Type Field Values	value	
+clinpath_types	Clinpath Type Field Values	value	
+clinremarks_category	Clinremarks Category Field Values	value	
+drug_categories	Drug Category Field Values	value	
+hematology_method	Hematology Method Field Values	value	
+problem_list_category	Problem List Category Field Values	value	
+parasitology_method	Parasitology Method Field Values	value	
+urinalysis_method	Urinalysis Method Field Values	value	
+urinalysis_qualitative_results	Urinalysis Qualitative Result Field Values	value	
+bcs_score	BCS Score Field Values	value	
+avail_codes Availability Code Field Values	value		
+status_codes	Status Code Field Values	value	
+snomed_qualifiers	SNOMED Code Qualifiers	value	
+housing_reason	Housing Reason Field Values	value	
+housing_condition_codes	Housing Condition Field Values	value	
+histology_stain	Histology Stain Field Values	value	
+encounter_types	Encounter Types	value	
+DeliveryMode	Delivery Mode Field Values	value	
+DeliveryType	Delivery Type Field Values	value	
+death_manner	Death Manner	value	
+death_cause	Death Cause	value	
+ConfirmationType	Pregnancy Confirmation Type	value	
+clinpath_collection_method	Clinpath Collection Method	value	

onprc_ehr/resources/data/pairing_observation_types.tsv

@@ -0,0 +1,6 @@
+value
+Divider Change
+Event
+Infant Related
+STF Beh
+STF Clinical

onprc_ehr/resources/data/pairingendtypes.tsv

@@ -0,0 +1,25 @@
+value
+All to group
+Contact decrease
+Contact increase
+Decrease contact
+Decrease partners
+End All Contact
+End clear
+End full contact
+End GC
+End group
+End large mesh
+Extended temporary separation.
+Increase contact
+Increase partners
+N/A
+Pair change-decrease.
+Pair change-increase.
+Pair to trio/group.
+Permanent Separation.
+Reunite from GC
+Temporary separation.
+TO with GC
+Unsuccessful attempt
+Unsuccessful set-up

onprc_ehr/resources/data/pairingpriorgroups.tsv

@@ -0,0 +1,3 @@
+value
+Not recent
+Recent

onprc_ehr/resources/data/pairingstarttype.tsv

@@ -0,0 +1,47 @@
+value
+Bio dam reunite
+C-sx reunite
+Contact decrease
+Contact Increase
+Contact increase first attempt
+Decrease partners
+Extended temporary separation
+Feeder Box
+General Comment
+Increase partners
+Increase partners first attempt
+Infant socialization
+Lactating foster
+Non BSU pair
+Nonlactating foster
+Pair attempt
+Pair change
+Pair change-decrease
+Pair change-increase
+Pair monitor
+Pair to trio/group
+Permanent separation
+Porch
+remote monitoring
+Reunite
+Reunite after procedure
+Reunite after TO
+Same social group pair
+Set up
+STE
+STF
+STF DNPC
+STF/E
+STF/E DNPC
+Temporary separation
+TMB
+TMB pair
+TO as GC
+trial contact
+trial contact first attempt
+Sep for Diet
+STE.
+STF.
+STF DNPC.
+STF/E.
+STF/E DNPC.

onprc_ehr/resources/queries/study/CageMateAdults.sql

@@ -0,0 +1,38 @@
+/*
+ * Copyright (c) 2017 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+SELECT
+
+    h1.Id,
+    group_concat(h2.Id, ' ') as adultcagemate,
+    group_Concat(distinct h2.room) as room,
+    group_concat(distinct h1.cage) as cage
+
+FROM study.demographicsCurrentLocation h1
+         JOIN study.demographicsCurrentLocation h2 ON (
+    h1.room = h2.room AND
+    h1.cage = h2.cage
+
+    )
+
+WHERE
+    h1.room.housingType.value = 'Cage Location' AND
+    h2.Id.age.ageInyears > 1
+
+
+GROUP BY h1.Id
+
+

onprc_ehr/resources/queries/study/CageMateAdults/.qview.xml

@@ -0,0 +1,5 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id" descending="false"/>
+    </sorts>
+</customView>

onprc_ehr/resources/queries/study/CageMateAll.sql

@@ -0,0 +1,37 @@
+/*
+ * Copyright (c) 2017 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+SELECT
+
+    h1.Id,
+    group_concat(h2.Id, '-') as adultcagemate,
+    group_Concat(distinct h2.room) as room,
+    group_concat(distinct h1.cage) as cage
+
+FROM study.demographicsCurrentLocation h1
+         JOIN study.demographicsCurrentLocation h2 ON (
+    h1.room = h2.room AND
+    h1.cage = h2.cage
+
+    )
+
+WHERE
+    h1.room.housingType.value = 'Cage Location'
+
+
+GROUP BY h1.Id
+
+

onprc_ehr/resources/queries/study/CageMateAll/.qview.xml

@@ -0,0 +1,5 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id" descending="false"/>
+    </sorts>
+</customView>

onprc_ehr/resources/queries/study/CageMateInfantpairings.sql

@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2017 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+SELECT
+
+    h1.Id,
+    group_concat(h2.Id, '-') as infantcagemate,
+    group_Concat(distinct h2.room) as room,
+    group_concat(distinct h1.cage) as cage
+
+FROM study.demographicsCurrentLocation h1
+         JOIN study.demographicsCurrentLocation h2 ON (
+    h1.room = h2.room AND
+    h1.cage = h2.cage
+
+    )
+
+WHERE
+    h1.room.housingType.value = 'Cage Location' AND
+    h2.Id.age.ageInyears < 1
+
+GROUP BY h1.Id

onprc_ehr/resources/queries/study/CageMateInfantpairings/.qview.xml

@@ -0,0 +1,5 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id" descending="false"/>
+    </sorts>
+</customView>