[bot] Merge 26.7 to 26.8

nbri_ehr/resources/data/birth_condition.tsv

@@ -0,0 +1,3 @@
+value	title	sort_order
+L	Live	1
+D	Dead	2

nbri_ehr/resources/data/breeding_type.tsv

@@ -0,0 +1,10 @@
+value	title	sort_order
+A	Assigned Breeding Protocol	1
+C	Cull	2
+H	Held from Mating Activity	3
+M	Multi-Male	4
+P	Project Breeding	5
+Q	Testing as Breeder	6
+S	Single Male Harem	7
+T	Time-Mated	8
+O	Not Assigned	9

nbri_ehr/resources/data/death_type.tsv

@@ -0,0 +1,14 @@
+value	title	sort_order
+A	Experimental	1
+D	Spontaneous/Normal	2
+F	Fetal	3
+FD	Fetal Death	4
+FL	Fetal Live	5
+FN	Fetal found at necropsy	6
+FX	Fetal experimental	7
+K	Cull (scheduled)	8
+M	Medical cull (non-scheduled)	9
+ND	Non-vaginal (C-section) dead	10
+NT	Not pregnant at assessment	11
+S	Cull	12
+X	Experimental	13

nbri_ehr/resources/data/delivery_mode.tsv

@@ -0,0 +1,4 @@
+value	title
+V	Vaginal
+N	Surgical-clinical
+NX	Surgical experimental

nbri_ehr/resources/data/editable_lookups.tsv

@@ -18,10 +18,12 @@ ehr_lookups	bcs_score	Clinical	Body Condition Score	Clinical observation fixed v
 ehr_lookups	behavior_abnormality	Clinical	Behavior Abnormality	Clinical observation fixed values.
 ehr_lookups	behavior_mgmt_codes	Behavior	Behavior Management Codes	Behavior observation fixed values.
 ehr_lookups	behavior_types	Behavior	Behavior Types	Behavior observation fixed values.
+ehr_lookups	birth_condition	Colony Management	Birth Condition	Birth condition values.
 ehr_lookups	blood_draw_reason	Clinical	Blood Draw Reason	Used in blood draw datasets.
 ehr_lookups	blood_draw_tube_type	Clinical	Blood Draw Tube Type	Used in blood draw datasets.
 ehr_lookups	blood_sample_type	Clinical	Blood Sample Types	Used in blood draw datasets.
 ehr_lookups	blood_tube_volumes	Clinical	Blood Tube Volumes	Used in blood draw datasets.
+ehr_lookups	breeding_type	Colony Management	Breeding Type	Breeding group assignment codes.
 ehr_lookups	cage_type	Colony Management	Cage Type	Used in cage details.
 ehr_lookups	calculated_status_codes	Colony Management	Calculated Status	Animal status values.
 ehr_lookups	capillary_refill_time	Clinical	Capillary Refill Times	Used clinical observations.
@@ -36,8 +38,10 @@ ehr_lookups	country	Colony Management	Country
 ehr_lookups	country_category	Colony Management	Country Category	
 ehr_lookups	daily_enrich_codes	Behavior	Daily enrichment codes.	
 ehr_lookups	data_category	Clinical	Data Categories	Used in datasets.
-ehr_lookups	death_reason	Colony Management	Death Reason	
-ehr_lookups	delivery_state	Colony Management	Delivery State	
+ehr_lookups	death_reason	Colony Management	Death Reason
+ehr_lookups	death_type	Colony Management	Death Type	Death type codes.
+ehr_lookups	delivery_mode	Colony Management	Delivery Mode
+ehr_lookups	delivery_state	Colony Management	Delivery State
 ehr_lookups	dental_obs	Clinical	Dental Observation Types	Clinical observation values.
 ehr_lookups	derm_obs	Clinical	Dermatologic Observation Types	Clinical observation values.
 ehr_lookups	digit_amputation	Clinical	Digit Amputation	Clinical observation fixed values.

nbri_ehr/resources/data/flag_categories.tsv

@@ -0,0 +1,11 @@
+Category	Description	Enforce Single Flag Per Animal?	Omit When Displaying Default Flags?	Highlight Flags of This Category?	Date Disabled
+Behavioral	Behavioral observations, abnormal-behavior designations and enrichment provided to the animal.	false	false	false	
+Capture	Restraint and handling limitations.	false	false	true	
+Clinical	Clinical conditions, procedures and veterinary designations.	false	false	false	
+Experimental	Experimental treatments, inoculations and implants.	false	false	true	
+Genetics	Genetic background, ancestry, inbreeding and genomic characterization.	false	true	false	
+Hold	Animal held or reserved for a specific project, investigator or shipment.	false	false	false	
+Reproduction	Breeding, contraception, pregnancy, fostering and rearing designations.	false	false	false	
+Socially housed	Social rank, pairing, group-formation and social-housing-exemption designations.	false	false	false	
+Status	Administrative status and availability designations.	false	false	true	
+Training	Training program participation and progress.	false	false	false	

nbri_ehr/resources/data/flag_values.tsv

@@ -0,0 +1,11 @@
+Category	Meaning	Description	Date Disabled	ObjectId
+Behavioral	Behavioral FLAG 1	Behavioral FLAG 1		
+Capture	Capture FLAG 1	Capture FLAG 1		
+Clinical	Clinical FLAG 1	Clinical FLAG 1		
+Experimental	Experimental FLAG 1	Experimental FLAG 1		
+Genetics	Genetics FLAG 1	Genetics FLAG 1		
+Hold	Hold FLAG 1	Hold FLAG 1		
+Reproduction	Reproduction FLAG 1	Reproduction FLAG 1		
+Socially housed	Socially housed FLAG 1	Socially housed FLAG 1		
+Status	Status FLAG 1	Status FLAG 1		
+Training	Training FLAG 1	Training FLAG 1		

nbri_ehr/resources/data/gender_codes.tsv

@@ -1,4 +1,4 @@
 code	meaning
-1	unknown
-2	female
-3	male
+U	Unknown
+F	Female
+M	Male

nbri_ehr/resources/data/lookup_sets.tsv

@@ -16,8 +16,10 @@ bcs_score	BCS Store	value	title
 behavior_abnormality	Behavior Abnormality	value
 behavior_mgmt_codes	Behavior Management Codes	value
 behavior_types	Behavior Types	value
+birth_condition	Birth Condition	value	title
 blood_draw_reason	Blood Draw Reason	value
 blood_sample_type	Blood Sample Types	value
+breeding_type	Breeding Type	value	title
 cage_type	Cage Type	value	title
 capillary_refill_time	Capillary Refill Time	value
 card_format	Card Format	value	title
@@ -31,6 +33,8 @@ country_category	Country Category	value	title
 daily_enrich_codes	Daily Enrichment Codes	value
 data_category	Data Category Field Values	value
 death_reason	Death Reason	value
+death_type	Death Type	value	title
+delivery_mode	Delivery Mode	value	title
 delivery_state	Delivery State	value	title
 dental_obs	Dental Observations	value
 derm_obs	Dermatologic Observations	value
@@ -98,6 +102,7 @@ req_order_type	Req Order Type	value	title
 respiratory_observations	Respiratory Observations	value	title
 sib_score	SIB Score	value
 skin_problem	Skin Problem	value
+status_codes	Status Code Field Values	value	title
 stool_score	Stool Score	value
 stool_types	Stool Types	value
 tb_obs_score	TB Obs Score	value

nbri_ehr/resources/data/lookupsManifest.tsv

@@ -18,10 +18,12 @@ bcs_score
 behavior_abnormality
 behavior_mgmt_codes
 behavior_types
+birth_condition
 blood_draw_reason
 blood_draw_tube_type
 blood_sample_type
 blood_tube_volumes
+breeding_type
 cage_type
 calculated_status_codes
 capillary_refill_time
@@ -35,6 +37,8 @@ country_category
 daily_enrich_codes
 data_category
 death_reason
+death_type
+delivery_mode
 delivery_state
 dental_obs
 derm_obs
@@ -51,6 +55,8 @@ expense_class
 fecal_score
 fecal_smear_score
 feed_assess_types
+flag_categories
+flag_values
 gastro_types
 gender_codes
 general_obs
@@ -108,7 +114,10 @@ routes
 sib_score
 source
 snomed
+species
+species_codes
 skin_problem
+status_codes
 stool_score
 stool_types
 tb_obs_score

nbri_ehr/resources/data/lookupsManifestTest.tsv

@@ -12,15 +12,18 @@ amount_units
 app_score
 arrival_type
 arthritis_types
+att_score
 bandage_observations
 bcs_score
 behavior_abnormality
 behavior_mgmt_codes
 behavior_types
+birth_condition
 blood_draw_reason
 blood_draw_tube_type
 blood_sample_type
 blood_tube_volumes
+breeding_type
 cage_type
 calculated_status_codes
 capillary_refill_time
@@ -34,6 +37,8 @@ country_category
 daily_enrich_codes
 data_category
 death_reason
+death_type
+delivery_mode
 delivery_state
 dental_obs
 derm_obs
@@ -50,6 +55,8 @@ expense_class
 fecal_score
 fecal_smear_score
 feed_assess_types
+flag_categories
+flag_values
 gastro_types
 gender_codes
 general_obs

nbri_ehr/resources/data/pregnancy_result.tsv

@@ -1,3 +1,7 @@
 value	title
-1	Stillborn
-2	Abort
+NT	No Tissue
+FD	Fetal Death
+FN	Found at necropsy
+FX	Live, Term, euthanized at birth
+ND	Live, Died day of birth (lungs inflated)
+FL	Fetal Delivery, live in Utero