Tighten birth and arrival entry and move lookup admin to one page

nbri_ehr/resources/data/editable_lookups.tsv

@@ -10,6 +10,7 @@ ehr_lookups	alopecia_type	Behavior	Alopecia Type	Behavior observation fixed valu
 ehr_lookups	alopecia_regrowth	Behavior	Alopecia Regrowth	Behavior observation fixed values.
 ehr_lookups	amount_units	Clinical	Amount Units	"Used in drugs, treatments given and treatments ordered datasets."
 ehr_lookups	app_score	Behavior	Appetite Score	Behavior observation fixed values.
+ehr_lookups	areas	Housing	Areas	Top level of the housing location hierarchy.
 ehr_lookups	arrival_type	Colony Management	Arrival Type	Types of arrivals.
 ehr_lookups	arthritis_types	Clinical	Arthritis Types	Clinical observation fixed values.
 ehr_lookups	att_score	Behavior	Attitude Score	Behavior observation fixed values.
@@ -23,6 +24,8 @@ ehr_lookups	blood_draw_tube_type	Clinical	Blood Draw Tube Type	Used in blood dra
 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	buildings	Housing	Buildings	Buildings within an area.
+ehr_lookups	cage	Housing	Cages	Cage locations within a room.
 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.
@@ -58,6 +61,7 @@ ehr_lookups	fecal_smear_score	Clinical	Fecal Smear Score	Clinical observation fi
 ehr_lookups	feed_assess_types	Behavior	Fecal Assessment Types	Behavior observation fixed values.
 ehr_lookups	flag_categories	Colony Management	Flag Categories	Used to specify flag behavior.
 ehr_lookups	flag_values	Colony Management	Flag Values	Animal flag values.
+ehr_lookups	floors	Housing	Floors	Floors within a building.
 ehr_lookups	gastro_types	Clinical	Gastrointestinal Types	Clinical observation fixed values.
 ehr_lookups	gender_codes	Colony Management	Sex Codes	Used in demographics dataset.
 ehr_lookups	general_obs	Clinical	General Observation Types	Clinical observation types.
@@ -69,6 +73,7 @@ ehr_lookups	housing_reason	Housing	Housing Move Reason	Used in housing dataset f
 ehr_lookups	hyd_score	Clinical	Hydration Score	Clinical observation fixed values.
 ehr_lookups	incision_score	Clinical	Incision Status	Clinical observation fixed values.
 ehr_lookups	indoor_outdoor	Colony Management	Indoor/Outdoor	Cage details
+ehr	investigators	Colony Management	Investigators	Investigators available for protocol and project assignment.
 ehr_lookups	keyword	Clinical	Keyword	Clinical observation fixed values.
 ehr_lookups	lameness	Clinical	Lameness	Clinical observation fixed values.
 ehr_lookups	mass_type	Clinical	Mass Type	Clinical observation fixed values.
@@ -102,6 +107,8 @@ ehr_lookups	procedure_category	Clinical	Procedure Category	Used in procedures to
 ehr_lookups	procedures	Clinical	Procedures	List of animal procedures.F
 ehr_lookups	problem_list_category	Clinical	Problem List Category	Used in problem list dataset. Set when opening a case.
 ehr_lookups	problem_list_subcategory	Clinical	Problem List Subcategory	Used in problem list to categorize problems.
+ehr	project	Colony Management	Projects	Projects animals can be assigned to.
+ehr	protocol	Colony Management	Protocols	IACUC protocols animals can be assigned to.
 ehr_lookups	protocol_category	Colony Management	Protocol Category	
 ehr_lookups	protocol_state	Colony Management	Protocol State	
 ehr_lookups	protocol_type	Colony Management	Protocol Type	
@@ -112,6 +119,7 @@ ehr_lookups	regulatory_stress_levels	Colony Management	Regulatory Stress Levels
 ehr_lookups	req_order_state	Colony Management	Request Order State	
 ehr_lookups	req_order_type	Colony Management	Request Order Type	
 ehr_lookups	respiratory_observations	Clinical	Respiratory Observations	Used in clinical observations.
+ehr_lookups	rooms	Housing	Rooms	Rooms within a building and floor.
 ehr_lookups	routes	Clinical	Treatment Routes	Used in drug and treatment datasets.
 ehr_lookups	sib_score	Behavior	SIB Score	Behavior observation fixed values.
 ehr_lookups	skin_problem	Clinical	Skin Problems	Clinical observation fixed values.

nbri_ehr/resources/data/source.tsv

@@ -1,103 +1,225 @@
 code	meaning
+ACCULAB	Acculab Life Sciences
+ABL	Advanced Bioscience Laboratories
+AECOM	Albert Einstein College of Medicine
+ALLERGAN	Allergan, Inc
+ALPHAGEN	Alpha Genesis
+ASU	Arizona State University
+AFRRI	Armed Forces Radiobiological Res.
 AAI	Asiatic Animal Imports
+BATTELLE	Battelle Research
+BCM	Baylor College of Medicine
+BEDFORD-VA	Bedford VA Hospital
 BIOQUAL	Bioqual, Incorporated
+BIOTOX	Biotox Sciences
+BLACKPOOL	Blackpool Zoological Gardens
+BOBCROW	Bob Crow (USDA 58B142)
+BOSTONU	Boston University
 BRANDEIS	Brandeis University
+BWH	Brigham and Women's Hospital
+BRISTOL	Bristol-Myers Company
+BRONX-VA	Bronx VA Hospital
+BWEF	BWEF-Primegen
 CA-DPH	Calif Dept Public Health Facilities
+CIMR	Calif. Institute for Medical Research
+CALTECH	California Institute of Technology
 CA-DOH	California State Department of Health
 CPRC	Carribean Primate Center
 CWRU	Case Western Reserve University
+CDC-GL	Center for Disease Control - Garcia.Lema
 UCD-CNS	Center for Neuroscience, UCD
 CR-KL	Charles River - Key Lois
 CRL	Charles River Labs
 CRRP	Charles River Research Primates Inc
 BROOKFIELD	Chicago Zoological Park (Brookfield Zoo)
 CHILDRENS	Childrens Hospital
+CHOP	Childrens Hospital of Philadelphia
 CHIMR	Christ Hospital Inst. for Medical Res.
+CMC	Colorado Mountain College
 CSU	Colorado State University
+COLUMBIA	Columbia University
+CONNAUGHT	Connaught Laboratories
 CORNELL	Cornell University
 COULSTON	Coulston Foundation
 COVANCE	Covance Research Products, Inc.
 PRIMGEN	CSP-Primgen
 CUTTER	Cutter Lab
+DHMRI	David H. Murdock Res Institute
 DMT	Del Mundo Trading
+DENVER-ZOO	Denver Zoological Gardens
+DODGE-ZOO	Dodge City Zoo
+DOHENY	Doheny Eye Foundation
+DOWNSTATE	Downstate Medical Center
+DUKE	Duke University Medical Center
 EPZ	El Paso Zoological Gardens
 ENVIGO	Envigo
+FOLSOM-ZOO	Folsom Zoo
+GENENTECH	Genentech, Inc.
 HAHNEMANN	Hahnemann University
 HL	Hazelton Laboratories
 HLA	Hazelton Laboratories America Inc.
+HEMKER-ZOO	Hemker Park and Zoo
+INDY-ZOO	Indianapolis Zoo
 UNK	Institution Unknown
 ISU-VDL	Iowa State Univ, Vet Diagnostic Lab
+ISIS	Isis Services
 JVL	Jan Vacek Limited
 JHMC	Jewish Hospital & Medical Center
+JHU	Johns Hopkins University
 JRI	Johnson Research Institute
 KNLPC	Kunming National Laboratory Primate Ctr.
 LABS	Laboratory Animal Breeders and Services
 LABSINDO	Labsindo
+LEGACY	Legacy Research Institute
 LEMSIP	LEMSIP, New York Medical Center, RDI
 LAIR	Letterman Army Res Inst-Presidio
 LB	Litton Bionetics
 LLU	Loma Linda University
+LSU-SOM	Louisiana State Univ School of Medicine
+MADIGAN	Madigan Army Center
+MWRI	Magee Womens Research Institute
+MIT	Massachusetts Institute of Technology
+MCW-ARC	Med College of Wisconsin, Anim Res Ctr
+MCG	Medical College of Georgia
+MEDRI	Medical Research Institute
+METRO-ZOO	Metro Richmond Zoo
 MSU-MI	Michigan State University
+MICKE-ZOO	Micke Grove Zoo
+MPLS-VA	Minneapolis Veterans Hospital
+MONKEYJNGL	Monkey Jungle
 MSU-MT	Montana State University
+MONTG-ZOO	Montgomery Zoo
+MOORPRK-ZO	Moorpark Zoo
+MSSM	Mount Sinai School of Medicine
 MPI	MPI Research
 NASA-ARC	NASA-Ames Research Center
+NIH	National Institutes of Health
 NAMRL	Naval Aerospace Medical Research Lab
+NEURALINK	Neuralink
+NSI	Neurosciences Institute
 NEPRC	New England Primate Research Center
+NMSU-PRI	New Mex State Univ, Primate Research Inst
+NICHOLS	Nichols Exotics
 NIHAC	NIH Animal Center
+NEU	Northeastern University
+NWU	Northwestern University
+OAKLAND-ZO	Oakland Zoo
+OSU	Ohio State University
+OHSU	Oregon Health Sciences University
+OPR	Oregon Primate Rescue
 ORPRC	Oregon Regional Primate Research Center
+OSAGE	Osage Research Primates
+PALOALTO-V	Palo Alto Veteran's Administration
 PARC-SAF	Parc Safari African
+PENN-ZOO	Pennington Zoo
 PPC	Perrine Primate Center
 PPP	Peruvian Primatological Project
 PET-FARM	Pet Farm
+PTDEF-ZOO	Point Defiance Zoo
 PRIMLAB	Primate Laboratory
 PPI	Primate Products, Incorporated
+PRINCETON	Princeton University
 PRIVATE	Private Party
 RIEPT	Res. Inst. of Exp. Pathology & Therapy
+SCRIPPS	Research Institute of Scripps Clinic
+RTI	Research Triangle Institute
+ROCKEFELLR	Rockefeller University
 SALK	Salk Institute
 SFGH	San Francisco General Hospital
+SFMC	San Francisco Medical Center
+SANTANA-ZO	Santa Ana Zoo
+SCHERING	Schering, Inc.
+SCIENCEXYZ	Science XYZ
+SHARP-CAB	Sharp Cabrillo Hospital
 SNBL	Shin Nippon Biomedical Laboratories
 SICONBREC	Siconbrec
 SBM	Sierra Biomedical
+SINCLAIR	Sinclair Research Center, LLC
 SKB	Smith, Kline, Beecham
+SKERI	Smith-Kettlewell Eye Research Institute
+SDPC	Sonora Desert Primate Conservancy
+STPO	South Texas Primate Observatory
 SIU	Southern Illinois University
 SIU-SOM	Southern Illinois University Med School
 SORI	Southern Research Institute
 SFRE	Southwest Foundation for Res. & Educ.
+SNPRC	Southwest Nat. Primate Center
 SWRF	Southwest Research Foundation
 SWRI	Southwest Research Institute
 SOPF	Stanford Outdoor Primate Facility
 SRI	Stanford Research Institute
+SU-ARF	Stanford University Animal Res. Facility
+SUNY-B	State Univ of New York at Buffalo
 SUNY-SB	State Univ of New York at Stony Brook
 SXZ	Suzhou Xishan Zhongke Lab Animal Co.
 SYNTEX	Syntex (USA) Incorporated
 TARPON	Tarpon Zoo
 TTUHSC	Texas Tech Health Science Center
 BROOKS-AFB	Texas, Brooks Air Force Base
 TPI	The Parkinson's Institute
+TJU	Thomas Jefferson University
 TNPRC	Tulane (Delta) Regional Primate Res Ctr
 UCB	UC Berkeley
 UCLA	UC Los Angeles
 UCR	UC Riverside
 UCSD	UC San Diego
 UCSF	UC San Francisco Vivarium
 UC-ARS	Univ of Calif, Animal Resources Service
+UC-DBS	Univ of Calif, Dept Biological Sci.
 GPC	Univ of Gottingen Primate Center
 UH-RAF	Univ of Hawaii, Research Animal Facility
+UMASS-MS	Univ of Massachusetts, Med School
 OUHSC	Univ of Oklahoma Health Sci. Center
+UTMB-G	Univ of Texas Medical Branch, Galveston
 UTHSC-H	Univ of Texas, Health Sci Ctr, Houston
+UTHSC	Univ. Texas Health Science Center
+UMDNJ	University Med/Dental of New Jersey
+UAB	University of Alabama, Birmingham
+UAZ	University of Arizona
+UBC	University of British Columbia
+UCI	University of California, Irvine
+UCHICAGO	University of Chicago
 UCHSC	University of Colorado Health Sciences
 UCMC	University of Colorado Medical Center
+UFL	University of Florida
+UGA	University of Georgia
 UIC	University of Illinois at Chicago
+UIOWA-OAK	University of Iowa, Oakdale Facility
+KUMC	University of Kansas Medical Center
+ULOUISVL	University of Louisville
+UMD	University of Maryland
+UMIAMI	University of Miami
+UMICH	University of Michigan
+UMN	University of Minnesota
+UMMC	University of Mississippi Medical Center
+MIZZOU	University of Missouri, Columbia
+UNMC	University of Nebraska Medical Center
 UNV	University of Nevada
 UNM	University of New Mexico
+UOREGON	University of Oregon
+UPENN	University of Pennsylvania
+PITT-DLAR	University of Pittsburgh Lab Animal Rscs
+PITT-SOM	University of Pittsburgh Medical School
 UPR	University of Puerto Rico
+USC	University of Southern California
+UTENN	University of Tennessee
 UTSCC	University of Texas System Cancer Center
+UTEP	University of Texas, El Paso
+UUMC	University of Utah Medical Center
 UNK-CN	Unknown Institution, China
+USC-LA	USC Livingston Annex
+VA	V.A. Hospital
 VBS	Valley Biosystems
+VANDERBILT	Vanderbilt University
+VCU	Virginia Commonwealth University
 WFSM	Wake Forest School of Medicine
 WANPRC	Washington Regional Primate Research Ctr
+WUSTL	Washington University School of Medicine
+WHITTAKER	Whittaker Bioproducts
 WHMC	Wilford Hall Medical Center
 WRPRC	Wisconsin Regional Primate Research Ctr
 WAI	Woodward Asiatic Imports
 WWP	World Wide Primates, Inc.
+YALE	Yale University
 YPRC	Yemassee Primate Research Center
+YRPRC	Yerkes Regional Primate Research Ctr

nbri_ehr/resources/data/species.tsv

@@ -2,12 +2,12 @@ Common	Scientific Name	Id Prefix	Mhc Prefix	Max Blood Draw (mL/kg)	Max Percent B
 Rhesus Macaque	Macaca Mulatta			3.0000	1.0000	7.0000
 Pig-Tailed Macaque	Macaca Nemestrina			3.0000	1.0000	7.0000
 Bonnet Macaque	Macaca Radiata			3.0000	1.0000	7.0000
-Olive Baboon	Papio Anubis			3.0000	1.0000	7.0000
+Olive Baboon	Papio Cynocephalus Anubis			3.0000	1.0000	7.0000
 Yellow Baboon	Papio Cynocephalus			3.0000	1.0000	7.0000
 Squirrel Monkey	Saimiri Sciureus			3.0000	1.0000	7.0000
 African Green Monkey	Chlorocebus Aethiops			3.0000	1.0000	7.0000
 Domestic Dog	Canis Familiaris			3.0000	1.0000	7.0000
-Formosan Rock Macaque	Macaca Cyclopis			3.0000	1.0000	7.0000
+Cynomolgus / Crab-Eating Macaque	Macaca Fascicularis			3.0000	1.0000	7.0000
 Japanese Macaque	Macaca Fuscata			3.0000	1.0000	7.000
 Talapoin Monkey	Cercopithecus Talapoin			3.0000	1.0000	7.0000
 Sykes' Monkey	Cercopithecus M Albogulari			3.0000	1.0000	7.0000

nbri_ehr/resources/data/species_codes.tsv

@@ -2,12 +2,12 @@ Code	Scientific Name	Common Name	Description	Genus	Species	Date Disabled
 MMU	Macaca Mulatta	Rhesus Macaque
 MNE	Macaca Nemestrina	Pig-Tailed Macaque
 MRA	Macaca Radiata	Bonnet Macaque
-PAN	Papio Anubis	Olive Baboon
+PAN	Papio Cynocephalus Anubis	Olive Baboon
 PCY	Papio Cynocephalus	Yellow Baboon
 SSC	Saimiri Sciureus	Squirrel Monkey
 CAE	Chlorocebus Aethiops	African Green / Vervet
 DOG	Canis Familiaris	Domestic Dog
-MCY	Macaca Cyclopis	Formosan Rock Macaque
+MCY	Macaca Fascicularis	Cynomolgus / Crab-Eating Macaque
 MFU	Macaca Fuscata	Japanese Macaque
 CTA	Cercopithecus Talapoin	Talapoin Monkey
 CMA	Cercopithecus M Albogulari	Sykes' Monkey

nbri_ehr/resources/domain-templates/ehr_lookups.template.xml

@@ -3,13 +3,30 @@
            xmlns:dat="http://labkey.org/data/xml"
            xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
 
+    <!-- The shared EHR schema gives areas and rooms a dateDisabled column but not buildings, floors, or
+         cages, so those three can only be deleted, never retired. Provisioned here so the whole housing
+         hierarchy can be disabled the same way. -->
     <template xsi:type="EHRLookupsTemplateType">
         <table tableName="buildings" tableDbType="TABLE">
             <dat:tableTitle>Buildings</dat:tableTitle>
             <dat:columns>
                 <dat:column columnName="area">
                     <dat:rangeURI>string</dat:rangeURI>
                 </dat:column>
+                <dat:column columnName="dateDisabled">
+                    <dat:rangeURI>dateTime</dat:rangeURI>
+                </dat:column>
+            </dat:columns>
+        </table>
+    </template>
+
+    <template xsi:type="EHRLookupsTemplateType">
+        <table tableName="floors" tableDbType="TABLE">
+            <dat:tableTitle>Floors</dat:tableTitle>
+            <dat:columns>
+                <dat:column columnName="dateDisabled">
+                    <dat:rangeURI>dateTime</dat:rangeURI>
+                </dat:column>
             </dat:columns>
         </table>
     </template>
@@ -35,6 +52,9 @@
                 <dat:column columnName="indoor_outdoor">
                     <dat:rangeURI>string</dat:rangeURI>
                 </dat:column>
+                <dat:column columnName="dateDisabled">
+                    <dat:rangeURI>dateTime</dat:rangeURI>
+                </dat:column>
             </dat:columns>
         </table>
     </template>

nbri_ehr/resources/queries/ehr_lookups/buildings.query.xml

@@ -16,6 +16,12 @@
                             <fkTable>areas</fkTable>
                             <fkColumnName>area</fkColumnName>
                             <fkDisplayColumnName>description</fkDisplayColumnName>
+                            <filters>
+                                <filterGroup>
+                                    <!-- Insert and update only, so a building whose area was retired afterward still displays it. -->
+                                    <filter column="dateDisabled" operator="isblank" value=""/>
+                                </filterGroup>
+                            </filters>
                         </fk>
                     </column>
                     <column columnName="name">

nbri_ehr/resources/queries/ehr_lookups/cage.query.xml

@@ -13,6 +13,12 @@
                             <fkDbSchema>ehr_lookups</fkDbSchema>
                             <fkTable>rooms</fkTable>
                             <fkColumnName>room</fkColumnName>
+                            <filters>
+                                <filterGroup>
+                                    <!-- Insert and update only, so a cage whose room was retired afterward still displays it. -->
+                                    <filter column="dateDisabled" operator="isblank" value=""/>
+                                </filterGroup>
+                            </filters>
                         </fk>
                     </column>
                     <column columnName="location">

nbri_ehr/resources/queries/ehr_lookups/floors.query.xml

@@ -13,6 +13,12 @@
                             <fkTable>buildings</fkTable>
                             <fkColumnName>name</fkColumnName>
                             <fkDisplayColumnName>description</fkDisplayColumnName>
+                            <filters>
+                                <filterGroup>
+                                    <!-- Insert and update only, so a floor whose building was retired afterward still displays it. -->
+                                    <filter column="dateDisabled" operator="isblank" value=""/>
+                                </filterGroup>
+                            </filters>
                         </fk>
                     </column>
                     <column columnName="floor">