diff --git a/nbri_ehr/resources/data/birth_condition.tsv b/nbri_ehr/resources/data/birth_condition.tsv new file mode 100644 index 0000000..bdb4e26 --- /dev/null +++ b/nbri_ehr/resources/data/birth_condition.tsv @@ -0,0 +1,3 @@ +value title sort_order +L Live 1 +D Dead 2 diff --git a/nbri_ehr/resources/data/breeding_type.tsv b/nbri_ehr/resources/data/breeding_type.tsv new file mode 100644 index 0000000..dea0f78 --- /dev/null +++ b/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 \ No newline at end of file diff --git a/nbri_ehr/resources/data/delivery_mode.tsv b/nbri_ehr/resources/data/delivery_mode.tsv new file mode 100644 index 0000000..cea8a58 --- /dev/null +++ b/nbri_ehr/resources/data/delivery_mode.tsv @@ -0,0 +1,4 @@ +value title +V Vaginal +N Surgical-clinical +NX Surgical experimental \ No newline at end of file diff --git a/nbri_ehr/resources/data/editable_lookups.tsv b/nbri_ehr/resources/data/editable_lookups.tsv index 90cc8af..1323d7b 100644 --- a/nbri_ehr/resources/data/editable_lookups.tsv +++ b/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. @@ -37,6 +39,7 @@ 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_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. @@ -61,6 +64,7 @@ ehr_lookups general_obs Clinical General Observation Types Clinical observation ehr_lookups genital_types Colony Management Genital Types Clinical observation fixed values. ehr_lookups genitourinary_obs Clinical Genitourinary Observation Types Clinical observation fixed values. ehr_lookups geographic_origins Colony Management Geographic Origins Used in demographics dataset. +ehr_lookups group_status Colony Management Group Status Group assignment status codes. ehr_lookups hernia_types Clinical Hernia Types Clinical observation fixed values. ehr_lookups housing_reason Housing Housing Move Reason Used in housing dataset for location transfers. ehr_lookups hyd_score Clinical Hydration Score Clinical observation fixed values. diff --git a/nbri_ehr/resources/data/gender_codes.tsv b/nbri_ehr/resources/data/gender_codes.tsv index 01c67fb..a55c8a7 100644 --- a/nbri_ehr/resources/data/gender_codes.tsv +++ b/nbri_ehr/resources/data/gender_codes.tsv @@ -1,4 +1,4 @@ code meaning -1 unknown -2 female -3 male \ No newline at end of file +U Unknown +F Female +M Male \ No newline at end of file diff --git a/nbri_ehr/resources/data/lookup_sets.tsv b/nbri_ehr/resources/data/lookup_sets.tsv index 613eb8e..993844b 100644 --- a/nbri_ehr/resources/data/lookup_sets.tsv +++ b/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 +33,7 @@ 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 +delivery_mode Delivery Mode value title delivery_state Delivery State value title dental_obs Dental Observations value derm_obs Dermatologic Observations value @@ -48,6 +51,7 @@ gastro_types Gastrointestinal Types value general_obs General Observations value genital_types Genital Types value genitourinary_obs Genitourinary Observations value +group_status Group Status value title hernia_types Hernia Types value housing_reason Housing Reason value hyd_score Hyd Score 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 diff --git a/nbri_ehr/resources/data/lookupsManifest.tsv b/nbri_ehr/resources/data/lookupsManifest.tsv index defb466..0dbf034 100644 --- a/nbri_ehr/resources/data/lookupsManifest.tsv +++ b/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 +37,7 @@ country_category daily_enrich_codes data_category death_reason +delivery_mode delivery_state dental_obs derm_obs @@ -57,6 +60,7 @@ general_obs genital_types genitourinary_obs geographic_origins +group_status hernia_types housing_reason hyd_score @@ -109,6 +113,7 @@ sib_score source snomed skin_problem +status_codes stool_score stool_types tb_obs_score diff --git a/nbri_ehr/resources/data/lookupsManifestTest.tsv b/nbri_ehr/resources/data/lookupsManifestTest.tsv index b2006c8..51c43a4 100644 --- a/nbri_ehr/resources/data/lookupsManifestTest.tsv +++ b/nbri_ehr/resources/data/lookupsManifestTest.tsv @@ -17,10 +17,12 @@ 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 @@ -34,6 +36,7 @@ country_category daily_enrich_codes data_category death_reason +delivery_mode delivery_state dental_obs derm_obs @@ -56,6 +59,7 @@ general_obs genital_types genitourinary_obs geographic_origins +group_status hernia_types housing_reason hyd_score diff --git a/nbri_ehr/resources/data/pregnancy_result.tsv b/nbri_ehr/resources/data/pregnancy_result.tsv index 1c615bc..819182e 100644 --- a/nbri_ehr/resources/data/pregnancy_result.tsv +++ b/nbri_ehr/resources/data/pregnancy_result.tsv @@ -1,3 +1,7 @@ value title -1 Stillborn -2 Abort \ No newline at end of file +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 \ No newline at end of file diff --git a/nbri_ehr/resources/data/source.tsv b/nbri_ehr/resources/data/source.tsv index 0d893c4..8dc42a1 100644 --- a/nbri_ehr/resources/data/source.tsv +++ b/nbri_ehr/resources/data/source.tsv @@ -1,108 +1,103 @@ code meaning -1 Adv Bioscience Labs -2 Alamogordo PrimateFaclty -3 Alpha Genesis, Inc. -4 Barton West End Farm -5 Battelle Memorial Inst -6 Baylor Research Inst -7 BIOCULTURE (MTIUS) LTD -8 Bioculture US LLC -9 BIOQUAL, Inc. -10 Boehringer Ingelheim -11 Boston University -12 Buckshire Corporation -13 Caribbean Primate Rsrch -14 CBNC -15 CDC -16 Charles River Laboratory -17 Charles River/Reno -18 Chimp Haven -19 China/Guangxi GF Sci Pri -20 Chiron Corp -21 CiToxLab North America -22 Covance Research Prod -23 CR Rsrch Models Houston -24 Ctr Captive Chimp Care -25 Cynologics Ltd -26 DHMRI -27 Duke Univ Medical Ctr -28 Durham Research Center -29 Emory University YPRC -30 Envigo Global Services -31 Guangdong Landau Biotech -32 Hainan, China -33 Harvard Medical School -34 Indonesia (Pt. W. Sat) -35 Johns Hopkins University -36 LC Preclinical Research -37 Lovelace Biomedical -38 LRRI -39 LSU Health Science BR -40 LSU Health Science NO -41 LSU Health Science Shv -42 Mannheimer Foundation -43 Mass. General Hospital -44 MD Anderson Cancer Ctr. -45 Merck & Co (Rahway) -46 Merck & Co (WP) -47 Merck Research Labs WP -48 Nationwide Children's -49 New England NPRC -50 New York University -51 NIAID (Bioqual) -52 NIAID Morgan Island -53 NIAID NIH Animal Ctr -54 NICHD/NIH -55 NIH -56 NIH Animal Center -57 NINDS NIH Animal Ctr -58 Novartis Pharm. Corp. -59 Novartis Vaccines Srl -60 NYU School of Medicine -61 Oregon NPRC -62 Pfizer -63 Pfizer-Andover -64 Pfizer-Pearl River -65 PreLabs -66 Primate Products -67 Primedica Labs -68 PrimGen -69 Primgen CSP -70 RainForest Adventures -71 Republic of Mauritius -72 Rocky Mountain Lab -73 Save the Chimps -74 Siconbrec Inc -75 Sierra Biomedical -76 SNBL-SRC -77 SRI International -78 St. Jude Childrens Rsrch -79 St. Kitts -80 Stanford Univ School Med -81 Stony Brook University -82 SUNY Downstate Medical -83 SW Found Biomed Rsrch -84 Texas Biomed -85 Three Springs Scientific -86 Tulane NPC (Covington) -87 Tulane Univ Medical Ctr -88 Univ Alabama Birmingham -89 Univ of Illinois -90 Univ of Kansas Med Ctr -91 Univ of Maryland -92 Univ of Nebraska Med Ctr -93 Univ of Pittsburgh -94 Univ of Texas at Austin -95 Univ of Washington NPRC -96 Univ of Wisconsin -97 Univ Tex MD Anderson CC -98 USAMRICD -99 USAMRIID -100 Virginia Commonwealth U -101 WakeForest School of Med -102 WaNPRC -103 Worldwide Primates, Inc. -104 WRAIR -105 Wyeth-Ayerst Rsrch (PR) -106 Yale Univ Sch Medicine -107 Yerkes Regional PRC \ No newline at end of file +AAI ASIATIC ANIMAL IMPORTS +BIOQUAL BIOQUAL, INCORPORATED +BRANDEIS BRANDEIS UNIVERSITY +CA-DPH CALIF DEPT PUBLIC HEALTH FACILITIES +CA-DOH CALIFORNIA STATE DEPARTMENT OF HEALTH +CPRC CARRIBEAN PRIMATE CENTER +CWRU CASE WESTERN RESERVE UNIVERSITY +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 +CHIMR CHRIST HOSPITAL INST. FOR MEDICAL RES. +CSU COLORADO STATE UNIVERSITY +CORNELL CORNELL UNIVERSITY +COULSTON COULSTON FOUNDATION +COVANCE COVANCE RESEARCH PRODUCTS, INC. +PRIMGEN CSP-PRIMGEN +CUTTER CUTTER LAB +DMT DEL MUNDO TRADING +EPZ EL PASO ZOOLOGICAL GARDENS +ENVIGO ENVIGO +HAHNEMANN HAHNEMANN UNIVERSITY +HL HAZELTON LABORATORIES +HLA HAZELTON LABORATORIES AMERICA INC. +UNK INSTITUTION UNKNOWN +ISU-VDL IOWA STATE UNIV, VET DIAGNOSTIC LAB +JVL JAN VACEK LIMITED +JHMC JEWISH HOSPITAL & MEDICAL CENTER +JRI JOHNSON RESEARCH INSTITUTE +KNLPC KUNMING NATIONAL LABORATORY PRIMATE CTR. +LABS LABORATORY ANIMAL BREEDERS AND SERVICES +LABSINDO LABSINDO +LEMSIP LEMSIP, NEW YORK MEDICAL CENTER, RDI +LAIR LETTERMAN ARMY RES INST-PRESIDIO +LB LITTON BIONETICS +LLU LOMA LINDA UNIVERSITY +MSU-MI MICHIGAN STATE UNIVERSITY +MSU-MT MONTANA STATE UNIVERSITY +MPI MPI RESEARCH +NASA-ARC NASA-AMES RESEARCH CENTER +NAMRL NAVAL AEROSPACE MEDICAL RESEARCH LAB +NEPRC NEW ENGLAND PRIMATE RESEARCH CENTER +NIHAC NIH ANIMAL CENTER +ORPRC OREGON REGIONAL PRIMATE RESEARCH CENTER +PARC-SAF PARC SAFARI AFRICAN +PPC PERRINE PRIMATE CENTER +PPP PERUVIAN PRIMATOLOGICAL PROJECT +PET-FARM PET FARM +PRIMLAB PRIMATE LABORATORY +PPI PRIMATE PRODUCTS, INCORPORATED +PRIVATE PRIVATE PARTY +RIEPT RES. INST. OF EXP. PATHOLOGY & THERAPY +SALK SALK INSTITUTE +SFGH SAN FRANCISCO GENERAL HOSPITAL +SNBL SHIN NIPPON BIOMEDICAL LABORATORIES +SICONBREC SICONBREC +SBM SIERRA BIOMEDICAL +SKB SMITH, KLINE, BEECHAM +SIU SOUTHERN ILLINOIS UNIVERSITY +SIU-SOM SOUTHERN ILLINOIS UNIVERSITY MED SCHOOL +SORI SOUTHERN RESEARCH INSTITUTE +SFRE SOUTHWEST FOUNDATION FOR RES. & EDUC. +SWRF SOUTHWEST RESEARCH FOUNDATION +SWRI SOUTHWEST RESEARCH INSTITUTE +SOPF STANFORD OUTDOOR PRIMATE FACILITY +SRI STANFORD RESEARCH INSTITUTE +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 +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 +GPC UNIV OF GOTTINGEN PRIMATE CENTER +UH-RAF UNIV OF HAWAII, RESEARCH ANIMAL FACILITY +OUHSC UNIV OF OKLAHOMA HEALTH SCI. CENTER +UTHSC-H UNIV OF TEXAS, HEALTH SCI CTR, HOUSTON +UCHSC UNIVERSITY OF COLORADO HEALTH SCIENCES +UCMC UNIVERSITY OF COLORADO MEDICAL CENTER +UIC UNIVERSITY OF ILLINOIS AT CHICAGO +UNV UNIVERSITY OF NEVADA +UNM UNIVERSITY OF NEW MEXICO +UPR UNIVERSITY OF PUERTO RICO +UTSCC UNIVERSITY OF TEXAS SYSTEM CANCER CENTER +UNK-CN UNKNOWN INSTITUTION, CHINA +VBS VALLEY BIOSYSTEMS +WFSM WAKE FOREST SCHOOL OF MEDICINE +WANPRC WASHINGTON REGIONAL PRIMATE RESEARCH CTR +WHMC WILFORD HALL MEDICAL CENTER +WRPRC WISCONSIN REGIONAL PRIMATE RESEARCH CTR +WAI WOODWARD ASIATIC IMPORTS +WWP WORLD WIDE PRIMATES, INC. +YPRC YEMASSEE PRIMATE RESEARCH CENTER diff --git a/nbri_ehr/resources/data/species.tsv b/nbri_ehr/resources/data/species.tsv index c95e4bd..12d3118 100644 --- a/nbri_ehr/resources/data/species.tsv +++ b/nbri_ehr/resources/data/species.tsv @@ -1,7 +1,15 @@ Common Scientific Name Id Prefix Mhc Prefix Max Blood Draw (mL/kg) Max Percent Blood Drawn Blood Reconstitution Interval (Days) Cites Code Date Disabled USDA Gestation -African Green Monkey Chlorocebus aethiops AGM 3.0000 1.0000 7.0000 -Brown-Tufted Capuchin Cebus apella CAP 3.0000 1.0000 7.0000 -Cynomolgus Macaque Macaca fascicularis CYN 3.0000 1.0000 7.0000 -Marmoset 3.0000 1.0000 7.0000 -Pig-Tailed Macaque Macaca nemestrina PIG 3.0000 1.0000 7.0000 -Rhesus Macaque Macaca mulatta RHM 3.0000 1.0000 7.0000 \ No newline at end of file +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 +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 +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 +Dusky Titi Monkey Callicebus Moloch 3.0000 1.0000 7.0000 +Brown-Tufted Capuchin Cebus Apella 3.0000 1.0000 7.0000 \ No newline at end of file diff --git a/nbri_ehr/resources/data/species_codes.tsv b/nbri_ehr/resources/data/species_codes.tsv index df698e7..feb4100 100644 --- a/nbri_ehr/resources/data/species_codes.tsv +++ b/nbri_ehr/resources/data/species_codes.tsv @@ -1,7 +1,15 @@ Code Scientific Name Common Name Description Genus Species Date Disabled -1 Chlorocebus aethiops AGM African Green Monkey 3 -10 Macaca mulatta RHM Rhesus Macaque 3 -18 Marmoset 3 -4 Cebus apella CAP Brown-Tufted Capuchin 3 -7 Macaca fascicularis CYN Cynomolgus Macaque 3 -9 Macaca nemestrina PIG Pig-Tailed Macaque 3 \ No newline at end of file +MMU Macaca Mulatta Rhesus Macaque +MNE Macaca Nemestrina Pig-Tailed Macaque +MRA Macaca Radiata Bonnet Macaque +PAN Papio 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 +MFU Macaca Fuscata Japanese Macaque +CTA Cercopithecus Talapoin Talapoin Monkey +CMA Cercopithecus M Albogulari Sykes' Monkey +CMO Callicebus Moloch Dusky Titi Monkey +CAP Cebus Apella Brown-Tufted Capuchin \ No newline at end of file diff --git a/nbri_ehr/resources/data/status_codes.tsv b/nbri_ehr/resources/data/status_codes.tsv new file mode 100644 index 0000000..b131086 --- /dev/null +++ b/nbri_ehr/resources/data/status_codes.tsv @@ -0,0 +1,5 @@ +value title +Alive Alive +Dead Dead +Escaped Escaped +Shipped Shipped diff --git a/nbri_ehr/resources/queries/ehr/project.query.xml b/nbri_ehr/resources/queries/ehr/project.query.xml index d2db2ca..5b72f21 100644 --- a/nbri_ehr/resources/queries/ehr/project.query.xml +++ b/nbri_ehr/resources/queries/ehr/project.query.xml @@ -47,6 +47,13 @@ true + + + core + Users + UserId + DisplayName + true diff --git a/nbri_ehr/resources/queries/nbri_ehr/Conception.query.xml b/nbri_ehr/resources/queries/nbri_ehr/Conception.query.xml index 0eb26a8..7fc6298 100644 --- a/nbri_ehr/resources/queries/nbri_ehr/Conception.query.xml +++ b/nbri_ehr/resources/queries/nbri_ehr/Conception.query.xml @@ -14,16 +14,28 @@ Conception Date - - Conception Date - Conception Term Date + + Estimated + Conception date is estimated rather than observed + true + + Task Id + ALWAYS_OFF + + ehr + tasks + taskid + rowid + + /ehr/dataEntryFormDetails.view?formType=${TaskId/formtype}&taskid=${TaskId} + Status @@ -31,6 +43,62 @@ qcstate rowid + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + + FBEC5D + + diff --git a/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.query.xml b/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.query.xml index 866a7da..8dac93d 100644 --- a/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.query.xml +++ b/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.query.xml @@ -11,9 +11,17 @@ Conception Id + + Estimated + Conception date is estimated rather than observed + Conception Outcome + + Offspring + Animals born from this conception, if a birth record references it + diff --git a/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.sql b/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.sql index 4554f1d..2890410 100644 --- a/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.sql +++ b/nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.sql @@ -8,16 +8,18 @@ SELECT c.ConceptId, c.ConceptDate, c.ConceptTermDate, + c.Estimated, c.Sire, CASE WHEN b.conceptId IS NOT NULL THEN 'Live Birth' WHEN po.conceptId IS NOT NULL THEN COALESCE(po.result, 'Unknown') ELSE 'Unknown' END AS conceptionOutcome, + b.offspring, c.Remark, c.QCState AS qcstate FROM Conception c -LEFT JOIN (SELECT DISTINCT b.conceptId FROM study.birth b WHERE b.conceptId IS NOT NULL) b +LEFT JOIN (SELECT b.conceptId, GROUP_CONCAT(DISTINCT b.Id, ', ') AS offspring FROM study.birth b WHERE b.conceptId IS NOT NULL GROUP BY b.conceptId) b ON b.conceptId = c.ConceptId LEFT JOIN (SELECT p.conceptId, MAX(p.result.title) AS result FROM study.pregnancy p WHERE p.conceptId IS NOT NULL GROUP BY p.conceptId) po ON po.conceptId = c.ConceptId diff --git a/nbri_ehr/resources/queries/study/arrival.js b/nbri_ehr/resources/queries/study/arrival.js index 251c651..2010ffd 100644 --- a/nbri_ehr/resources/queries/study/arrival.js +++ b/nbri_ehr/resources/queries/study/arrival.js @@ -40,7 +40,6 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even row.birth = row['Id/demographics/birth'] || null; row.gender = row['Id/demographics/gender'] || null; row.geographic_origin = row['Id/demographics/geographic_origin'] || null; - row.source = row.sourceFacility || null; if (row.QCStateLabel) { row.qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId(); diff --git a/nbri_ehr/resources/queries/study/arrival.query.xml b/nbri_ehr/resources/queries/study/arrival.query.xml index ffe2108..0955496 100644 --- a/nbri_ehr/resources/queries/study/arrival.query.xml +++ b/nbri_ehr/resources/queries/study/arrival.query.xml @@ -66,7 +66,8 @@ ehr_lookups source - meaning + code + meaning diff --git a/nbri_ehr/resources/queries/study/birth.js b/nbri_ehr/resources/queries/study/birth.js index e3e5fd0..cd0cce1 100644 --- a/nbri_ehr/resources/queries/study/birth.js +++ b/nbri_ehr/resources/queries/study/birth.js @@ -38,7 +38,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even //when updating a record that already carries this conception id, the existing row accounts for one match var conceptIdThreshold = (oldRow && oldRow.conceptId === row.conceptId) ? 1 : 0; if (triggerHelper.totalRecords('study', 'birth', 'conceptId', row.conceptId) > conceptIdThreshold) { - EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id is already used by another birth record', 'INFO'); + EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id is already used by another birth record', 'WARN'); } if (triggerHelper.totalRecords('study', 'pregnancy', 'conceptId', row.conceptId) > 0) { diff --git a/nbri_ehr/resources/queries/study/birth.query.xml b/nbri_ehr/resources/queries/study/birth.query.xml index 8eccc34..18a5a92 100644 --- a/nbri_ehr/resources/queries/study/birth.query.xml +++ b/nbri_ehr/resources/queries/study/birth.query.xml @@ -8,11 +8,18 @@ - - + Birth Date + + Conception Id + + nbri_ehr + Conception + ConceptId + + Birth Location 80 @@ -25,6 +32,25 @@ cage + + Delivery Mode + false + + ehr_lookups + delivery_mode + value + title + + + + Birth Condition + + ehr_lookups + birth_condition + value + title + + Project @@ -43,12 +69,13 @@ title - - Conception Id + + Breeding Type - nbri_ehr - Conception - ConceptId + ehr_lookups + breeding_type + value + title diff --git a/nbri_ehr/resources/queries/study/demographics.query.xml b/nbri_ehr/resources/queries/study/demographics.query.xml index bff3d17..f6fafa6 100644 --- a/nbri_ehr/resources/queries/study/demographics.query.xml +++ b/nbri_ehr/resources/queries/study/demographics.query.xml @@ -99,9 +99,6 @@ meaning - - Source - CITES diff --git a/nbri_ehr/resources/queries/study/demographics/.qview.xml b/nbri_ehr/resources/queries/study/demographics/.qview.xml index 56f1f23..439cd0a 100644 --- a/nbri_ehr/resources/queries/study/demographics/.qview.xml +++ b/nbri_ehr/resources/queries/study/demographics/.qview.xml @@ -12,7 +12,6 @@ - diff --git a/nbri_ehr/resources/queries/study/demographicsSource.sql b/nbri_ehr/resources/queries/study/demographicsSource.sql index 9de9dfd..6ee341e 100644 --- a/nbri_ehr/resources/queries/study/demographicsSource.sql +++ b/nbri_ehr/resources/queries/study/demographicsSource.sql @@ -17,7 +17,7 @@ SELECT WHEN T1.EarliestArrival IS NULL AND d.birth IS NOT NULL THEN true ELSE false END as fromCenter, - d.source as source, + T2.sourceFacility as source, CASE WHEN T1.EarliestArrival IS NULL AND d.birth IS NOT NULL THEN 'Born at NBRI' diff --git a/nbri_ehr/resources/queries/study/departure.query.xml b/nbri_ehr/resources/queries/study/departure.query.xml index 19845d1..5955592 100644 --- a/nbri_ehr/resources/queries/study/departure.query.xml +++ b/nbri_ehr/resources/queries/study/departure.query.xml @@ -13,7 +13,8 @@ ehr_lookups source - meaning + code + meaning diff --git a/nbri_ehr/resources/queries/study/protocolAssignment.query.xml b/nbri_ehr/resources/queries/study/protocolAssignment.query.xml index ac61d1c..d95eb07 100644 --- a/nbri_ehr/resources/queries/study/protocolAssignment.query.xml +++ b/nbri_ehr/resources/queries/study/protocolAssignment.query.xml @@ -15,7 +15,6 @@ ehr protocol protocol - title diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml index 55e48ea..42317f7 100644 --- a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -224,6 +224,15 @@ varchar + + varchar + + + varchar + + + varchar + @@ -469,9 +478,6 @@ varchar - - varchar - varchar diff --git a/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-26.000-26.001.sql b/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-26.000-26.001.sql index 964b91c..866fefc 100644 --- a/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-26.000-26.001.sql +++ b/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-26.000-26.001.sql @@ -9,6 +9,7 @@ CREATE TABLE nbri_ehr.Conception ConceptId VARCHAR(100), ConceptDate TIMESTAMP, ConceptTermDate TIMESTAMP, + Estimated BOOLEAN DEFAULT FALSE, Remark TEXT, Dam VARCHAR(100), Sire VARCHAR(100), diff --git a/nbri_ehr/resources/schemas/nbri_ehr.xml b/nbri_ehr/resources/schemas/nbri_ehr.xml index 6d076c8..2bc125d 100644 --- a/nbri_ehr/resources/schemas/nbri_ehr.xml +++ b/nbri_ehr/resources/schemas/nbri_ehr.xml @@ -581,6 +581,7 @@ Date + diff --git a/nbri_ehr/resources/scripts/nbri_triggers.js b/nbri_ehr/resources/scripts/nbri_triggers.js index e4ad95b..190f656 100644 --- a/nbri_ehr/resources/scripts/nbri_triggers.js +++ b/nbri_ehr/resources/scripts/nbri_triggers.js @@ -40,9 +40,15 @@ exports.init = function (EHR) { }); }); + // the arrival and birth forms assign animals that do not have a demographics record yet, so those forms ask for Id validation to be relaxed + function isAllowAnyIdRequested(helper) { + helper.decodeExtraContextProperty('allowAnyId', false); + return helper.getProperty('allowAnyId') === true; // this can be true or an empty object + } + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'protocolAssignment', function(event, helper) { helper.setScriptOptions({ - allowAnyId: false, + allowAnyId: isAllowAnyIdRequested(helper), requiresStatusRecalc: false, allowDatesInDistantPast: true }); @@ -50,7 +56,7 @@ exports.init = function (EHR) { EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'assignment', function(event, helper) { helper.setScriptOptions({ - allowAnyId: false, + allowAnyId: isAllowAnyIdRequested(helper), requiresStatusRecalc: false, allowDatesInDistantPast: true, skipAssignmentCheck: true, diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/Arrival.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/Arrival.js index 3e2850b..a5e983f 100644 --- a/nbri_ehr/resources/web/nbri_ehr/model/sources/Arrival.js +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/Arrival.js @@ -25,7 +25,7 @@ EHR.model.DataModelManager.registerMetadata('Arrival', { byQuery: { 'study.arrival': { 'cage': { - allowBlank: false, + // allowBlank: false, columnConfig: { fixed: true, width: 200 @@ -39,45 +39,28 @@ EHR.model.DataModelManager.registerMetadata('Arrival', { allowBlank: false }, 'Id/demographics/birth': { - allowBlank: false + // allowBlank: false }, 'Id/demographics/gender': { allowBlank: false }, 'Id/demographics/geographic_origin': { - allowBlank: false, + // allowBlank: false, columnConfig: { fixed: true, width: 200 } }, + // project and protocol are entered through the Project Assignment and Protocol Assignment sections project: { - xtype: 'combo', - columnConfig: { - width: 150 - }, - lookup: { - schemaName: 'ehr', - queryName: 'project', - keyColumn: 'project', - columns: 'project,name', - filterArray: [ - LABKEY.Filter.create('isActive', true, LABKEY.Filter.Types.EQUAL), - ] - }, - allowBlank: false + allowBlank: true, + hidden: true, + showInGrid: false }, arrivalProtocol: { - allowBlank: false, - columnConfig: { - width: 200 - }, - lookup: { - schemaName: 'ehr', - queryName: 'activeProtocols', - keyColumn: 'protocol', - columns: 'protocol,title' - }, + allowBlank: true, + hidden: true, + showInGrid: false }, performedby: { hidden: true, @@ -91,14 +74,14 @@ EHR.model.DataModelManager.registerMetadata('Arrival', { }, }, acquisitionType: { - allowBlank: false, + // allowBlank: false, columnConfig: { fixed: true, width: 150 }, }, arrivalType: { - allowBlank: false, + // allowBlank: false, columnConfig: { width: 200 } diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js index 4db08ad..4d38d3c 100644 --- a/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js @@ -37,12 +37,14 @@ EHR.model.DataModelManager.registerMetadata('Assignment', { fixed: true, width: 150 }, + // set displayColumn: ehr.protocol's title column (displayName) is not returned by this query lookup: { schemaName: 'ehr', queryName: 'activeProtocols', keyColumn: 'protocol', + displayColumn: 'protocol', columns: 'protocol,title' - }, + } } } } diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/Birth.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/Birth.js index 7202b23..f266f1e 100644 --- a/nbri_ehr/resources/web/nbri_ehr/model/sources/Birth.js +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/Birth.js @@ -24,58 +24,68 @@ EHR.model.DataModelManager.registerMetadata('Birth', { }, byQuery: { 'study.birth': { + Id: { + allowBlank: false, + nullable: false + }, + date: { + allowBlank: false, + nullable: false + }, 'Id/demographics/species': { allowBlank: false, + nullable: false, columnConfig: { fixed: true, width: 250 } }, 'cage': { - allowBlank: false, + // allowBlank: false, columnConfig: { fixed: true, width: 200 }, }, - project: { - xtype: 'combo', - allowBlank: false, + type: { columnConfig: { - width: 150 + width: 200 }, - lookup: { - schemaName: 'ehr', - queryName: 'project', - keyColumn: 'project', - columns: 'project,name', - filterArray: [ - LABKEY.Filter.create('isActive', true, LABKEY.Filter.Types.EQUAL), - ] - } }, - birthProtocol: { + cond: { columnConfig: { width: 200 }, - allowBlank: false, - lookup: { - schemaName: 'ehr', - queryName: 'activeProtocols', - keyColumn: 'protocol', - columns: 'protocol,title' - }, + }, + // project and protocol are entered through the Project Assignment and Protocol Assignment sections + project: { + allowBlank: true, + hidden: true, + showInGrid: false + }, + birthProtocol: { + allowBlank: true, + hidden: true, + showInGrid: false }, 'Id/demographics/birth': { allowBlank: false }, 'Id/demographics/gender': { - allowBlank: false + allowBlank: false, + nullable: false }, conceptId: { + allowBlank: false, + nullable: false, columnConfig: { width: 150 } + }, + breedingType: { + columnConfig: { + width: 200 + } } } } diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/Conception.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/Conception.js index d862181..949d8cb 100644 --- a/nbri_ehr/resources/web/nbri_ehr/model/sources/Conception.js +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/Conception.js @@ -35,6 +35,13 @@ EHR.model.DataModelManager.registerMetadata('Conception', { width: 200 }, }, + Estimated: { + xtype: 'checkbox', + defaultValue: false, + columnConfig: { + width: 100 + }, + }, Dam: { xtype: 'ehr-animalfield', lookups: false, diff --git a/nbri_ehr/resources/web/nbri_ehr/window/StartWithConceptionWindow.js b/nbri_ehr/resources/web/nbri_ehr/window/StartWithConceptionWindow.js new file mode 100644 index 0000000..4c2bb0f --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/window/StartWithConceptionWindow.js @@ -0,0 +1,137 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +/** + * Adds a birth record pre-populated from an existing conception record. + * + * @cfg {Object} targetStore + * @cfg {Object} formConfig + */ +Ext4.define('NBRI_EHR.window.StartWithConceptionWindow', { + extend: 'Ext.window.Window', + + initComponent: function(){ + Ext4.apply(this, { + title: 'Start with Conception', + modal: true, + closeAction: 'destroy', + border: true, + bodyStyle: 'padding: 5px', + width: 400, + defaults: { + border: false, + width: 370 + }, + items: [{ + html: 'Select a conception record. A new birth record will be added using the conception Id, along with the dam, sire and species from that conception.', + style: 'padding-bottom: 10px;' + },{ + xtype: 'labkey-combo', + itemId: 'conceptionField', + fieldLabel: 'Conception Id', + displayField: 'ConceptId', + valueField: 'ConceptId', + forceSelection: true, + queryMode: 'local', + anyMatch: true, + caseSensitive: false, + store: { + type: 'labkey-store', + schemaName: 'nbri_ehr', + queryName: 'Conception', + columns: 'ConceptId,ConceptDate,Dam,Sire', + sort: '-ConceptDate', + autoLoad: true + } + }], + buttons: [{ + text: 'Submit', + scope: this, + handler: this.onSubmit + },{ + text: 'Close', + handler: function(btn){ + btn.up('window').close(); + } + }] + }); + + this.callParent(arguments); + }, + + onSubmit: function(btn){ + var field = this.down('#conceptionField'); + var conceptId = field.getValue(); + if (!conceptId){ + Ext4.Msg.alert('Error', 'Must select a conception Id'); + return; + } + + var record = field.findRecordByValue(conceptId); + if (!record){ + Ext4.Msg.alert('Error', 'Unable to find the conception record for: ' + conceptId); + return; + } + + var dam = record.get('Dam'); + var sire = record.get('Sire'); + + btn.disable(); + this.getSpecies(dam, function(species){ + this.addRow(conceptId, dam, sire, species); + btn.enable(); + this.close(); + }, this); + }, + + // the species of the offspring is inferred from the dam of the conception + getSpecies: function(dam, callback, scope){ + if (!dam){ + callback.call(scope, null); + return; + } + + LABKEY.Query.selectRows({ + schemaName: 'study', + queryName: 'demographics', + columns: 'Id,species', + filterArray: [LABKEY.Filter.create('Id', dam, LABKEY.Filter.Types.EQUAL)], + scope: this, + success: function(results){ + var species = results.rows && results.rows.length ? results.rows[0].species : null; + callback.call(scope, species); + }, + failure: function(error){ + console.error(error); + callback.call(scope, null); + } + }); + }, + + addRow: function(conceptId, dam, sire, species){ + this.targetStore.add(this.targetStore.createModel({ + conceptId: conceptId, + 'Id/demographics/dam': dam, + 'Id/demographics/sire': sire, + 'Id/demographics/species': species + })); + } +}); + +EHR.DataEntryUtils.registerGridButton('NBRI_START_WITH_CONCEPTION', function(config){ + return Ext4.Object.merge({ + text: 'Start with Conception', + tooltip: EHR.DataEntryUtils.shouldShowTooltips() ? 'Click to add a birth record populated from an existing conception record' : undefined, + handler: function(btn){ + var grid = btn.up('gridpanel'); + + Ext4.create('NBRI_EHR.window.StartWithConceptionWindow', { + targetStore: grid.store, + formConfig: grid.formConfig + }).show(); + } + }, config); +}); diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIArrivalFormType.java b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIArrivalFormType.java index b79b90b..61fe238 100644 --- a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIArrivalFormType.java +++ b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIArrivalFormType.java @@ -23,6 +23,8 @@ import org.labkey.nbri_ehr.dataentry.section.NBRIAnimalDetailsFormSection; import org.labkey.nbri_ehr.dataentry.section.NBRIArrivalFormSection; import org.labkey.nbri_ehr.dataentry.section.NBRIArrivalInstructionsFormSection; +import org.labkey.nbri_ehr.dataentry.section.NBRIProjectAssignmentFormSection; +import org.labkey.nbri_ehr.dataentry.section.NBRIProtocolAssignmentFormSection; import org.labkey.nbri_ehr.dataentry.section.NBRITaskFormSection; import org.labkey.nbri_ehr.dataentry.section.NBRIWeightFormSection; @@ -40,13 +42,17 @@ public NBRIArrivalFormType(DataEntryFormContext ctx, Module owner) new NBRITaskFormSection(), new NBRIAnimalDetailsFormSection(), new NBRIArrivalFormSection(), + new NBRIProtocolAssignmentFormSection(true, true, true), + new NBRIProjectAssignmentFormSection(true, true, true), new NBRIWeightFormSection(true, true) )); + addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/model/sources/Assignment.js")); addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/model/sources/Arrival.js")); for (FormSection s : getFormSections()) { + s.addConfigSource("Assignment"); s.addConfigSource("Arrival"); } diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBirthFormType.java b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBirthFormType.java index ebe9c2b..cbd66ea 100644 --- a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBirthFormType.java +++ b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBirthFormType.java @@ -24,6 +24,8 @@ import org.labkey.nbri_ehr.dataentry.section.NBRIAnimalDetailsFormSection; import org.labkey.nbri_ehr.dataentry.section.NBRIBirthFormSection; import org.labkey.nbri_ehr.dataentry.section.NBRIBirthInstructionsFormSection; +import org.labkey.nbri_ehr.dataentry.section.NBRIProjectAssignmentFormSection; +import org.labkey.nbri_ehr.dataentry.section.NBRIProtocolAssignmentFormSection; import org.labkey.nbri_ehr.dataentry.section.NBRITaskFormSection; import java.util.ArrayList; @@ -39,16 +41,20 @@ public NBRIBirthFormType (DataEntryFormContext ctx, Module owner) new NBRIBirthInstructionsFormSection(), new NBRITaskFormSection(), new NBRIAnimalDetailsFormSection(), - new NBRIBirthFormSection() + new NBRIBirthFormSection(), + new NBRIProtocolAssignmentFormSection(true, true, true), + new NBRIProjectAssignmentFormSection(true, true, true) )); addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/plugin/RowEditor.js")); addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/model/sources/NBRIDefault.js")); + addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/model/sources/Assignment.js")); addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/model/sources/Birth.js")); addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/window/AddAnimalsWindow.js")); for (FormSection s : getFormSections()) { + s.addConfigSource("Assignment"); s.addConfigSource("Birth"); } } diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIBirthFormSection.java b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIBirthFormSection.java index 604cbb9..ddecd53 100644 --- a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIBirthFormSection.java +++ b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIBirthFormSection.java @@ -22,15 +22,34 @@ import org.labkey.api.query.FieldKey; import org.labkey.api.view.template.ClientDependency; +import java.util.ArrayList; import java.util.List; public class NBRIBirthFormSection extends NewAnimalFormSection { + // left to right column order of the Births grid; the demographics fields are not on study.birth, so they are added here + private static final List COLUMN_ORDER = List.of( + FieldKey.fromString("Id"), + FieldKey.fromString("date"), + FieldKey.fromString("conceptId"), + FieldKey.fromString("Id/demographics/species"), + FieldKey.fromString("Id/demographics/gender"), + FieldKey.fromString("Id/demographics/dam"), + FieldKey.fromString("Id/demographics/sire"), + FieldKey.fromString("cage"), + FieldKey.fromString("type"), + FieldKey.fromString("cond"), + FieldKey.fromString("breedingType"), + FieldKey.fromString("remark"), + FieldKey.fromString("performedby") + ); + public NBRIBirthFormSection() { super("study", "birth", "Births", false); addClientDependency(ClientDependency.supplierFromPath("ehr/window/FormBulkAddWindow.js")); addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/window/FormBulkAddWindow.js")); + addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/window/StartWithConceptionWindow.js")); } @Override @@ -46,14 +65,12 @@ public JSONObject toJSON(DataEntryFormContext ctx, boolean includeFormElements) @Override protected List getFieldKeys(TableInfo ti) { - List keys = super.getFieldKeys(ti); + List ordered = new ArrayList<>(COLUMN_ORDER); - keys.add(2, FieldKey.fromString("Id/demographics/species")); - keys.add(3, FieldKey.fromString("Id/demographics/gender")); - keys.add(4, FieldKey.fromString("Id/demographics/dam")); - keys.add(5, FieldKey.fromString("Id/demographics/sire")); + // anything not explicitly ordered above (hidden and system fields) keeps its default position at the end + super.getFieldKeys(ti).stream().filter(key -> !COLUMN_ORDER.contains(key)).forEach(ordered::add); - return keys; + return ordered; } @Override @@ -68,6 +85,7 @@ public List getTbarButtons() defaultButtons.add(idx, "NBRI_ADDANIMALS"); } defaultButtons.remove("COPYFROMSECTION"); + defaultButtons.addFirst("NBRI_START_WITH_CONCEPTION"); return defaultButtons; } 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 38aa173..38fd24d 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 @@ -751,7 +751,7 @@ public void doSharedCustomization(AbstractTableInfo ti) { UserSchema us = getEHRUserSchema(ti, "ehr_lookups"); col.setLabel("Species"); - col.setFk(new QueryForeignKey(ti.getUserSchema(), ti.getContainerFilter(), us, null, "species_codes", "code", "scientific_name")); + col.setFk(new QueryForeignKey(ti.getUserSchema(), ti.getContainerFilter(), us, null, "species_codes", "code", "common_name")); } if ("protocol".equalsIgnoreCase(col.getName()) && null == col.getFk() && !"protocol".equalsIgnoreCase(ti.getName())) { 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 c7587ae..93eb777 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 @@ -363,13 +363,13 @@ private void addNBRIEhrLinks() @Override protected String getMale() { - return "3"; + return "M"; } @Override protected String getFemale() { - return "2"; + return "F"; } @Test @@ -576,13 +576,24 @@ public void testArrivalForm() arrivals.setGridCell(1, "acquisitionType", "Lab Transfer (Wild Born)"); arrivals.setGridCell(1, "Id", arrivedAnimal); arrivals.setGridCell(1, "cage", "C1"); - arrivals.setGridCell(1, "project", "640991"); - arrivals.setGridCell(1, "arrivalProtocol", "dummyprotocol"); - arrivals.setGridCell(1, "Id/demographics/gender", "female"); + arrivals.setGridCell(1, "Id/demographics/gender", "Female"); arrivals.setGridCell(1, "Id/demographics/geographic_origin", "BRAZIL"); - arrivals.setGridCell(1, "Id/demographics/species", "Macaca nemestrina PIG"); + arrivals.setGridCell(1, "Id/demographics/species", "Pig-Tailed Macaque"); arrivals.setGridCellJS(1, "Id/demographics/birth", now.minusDays(7).format(DateTimeFormatter.ofPattern(DATE_TIME_FORMAT_STRING))); - arrivals.setGridCell(1, "sourceFacility", "BIOQUAL, Inc."); + arrivals.setGridCell(1, "sourceFacility", "BIOQUAL, INCORPORATED"); + + Ext4GridRef protocolAssignments = _helper.getExt4GridForFormSection("Protocol Assignment"); + _helper.addRecordToGrid(protocolAssignments); + protocolAssignments.setGridCell(1, "Id", arrivedAnimal); + protocolAssignments.setGridCellJS(1, "date", now.minusDays(1).format(DateTimeFormatter.ofPattern(DATE_TIME_FORMAT_STRING))); + protocolAssignments.setGridCell(1, "protocol", "dummyprotocol"); + + Ext4GridRef projectAssignments = _helper.getExt4GridForFormSection("Project Assignment"); + _helper.addRecordToGrid(projectAssignments); + projectAssignments.setGridCell(1, "Id", arrivedAnimal); + projectAssignments.setGridCellJS(1, "date", now.minusDays(1).format(DateTimeFormatter.ofPattern(DATE_TIME_FORMAT_STRING))); + projectAssignments.setGridCell(1, "project", "640991"); + submitForm("Submit Final", "Finalize"); goToSchemaBrowser(); @@ -590,13 +601,19 @@ public void testArrivalForm() table.setFilter("Id", "Equals", arrivedAnimal); CustomizeView view = table.openCustomizeGrid(); view.addColumn("cage"); - view.addColumn("project"); - view.addColumn("arrivalProtocol"); view.applyCustomView(); Assert.assertEquals("Invalid Arrival record", Arrays.asList(arrivedAnimal), table.getRowDataAsText(0, "Id")); Assert.assertEquals("Invalid Arrival record", Arrays.asList("C1"), table.getRowDataAsText(0, "cage")); - Assert.assertEquals("Invalid Arrival record", Arrays.asList("640991"), table.getRowDataAsText(0, "project")); - Assert.assertEquals("Invalid Arrival record", Arrays.asList("dummyprotocol"), table.getRowDataAsText(0, "arrivalProtocol")); + + goToSchemaBrowser(); + table = viewQueryData("study", "assignment"); + table.setFilter("Id", "Equals", arrivedAnimal); + Assert.assertEquals("Invalid project assignment", Arrays.asList("640991"), table.getRowDataAsText(0, "project")); + + goToSchemaBrowser(); + table = viewQueryData("study", "protocolAssignment"); + table.setFilter("Id", "Equals", arrivedAnimal); + Assert.assertEquals("Invalid protocol assignment", Arrays.asList("dummyprotocol"), table.getRowDataAsText(0, "protocol")); verifyRowCreated("study", "birth", arrivedAnimal, 1); verifyRowCreated("study", "assignment", arrivedAnimal, 1); @@ -606,15 +623,24 @@ public void testArrivalForm() } @Test - public void testBirthForm() throws IOException, CommandException + public void testBirthForm() throws Exception { String bornAnimal = "80801"; + String damId = "TESTDAM01"; + String sireId = "TESTSIRE01"; + // demographics.species holds an ehr_lookups.species_codes code; the grids display its common name + String damSpeciesCode = "CAP"; + String damSpecies = "Brown-Tufted Capuchin"; String conceptId = "TESTCONCEPT1"; + String breedingType = "Time-Mated"; LocalDateTime now = LocalDateTime.now(); + log("Creating the dam and sire of the conception"); + createBreedingPair(damId, sireId, damSpeciesCode); + log("Creating conception record"); InsertRowsCommand conception = new InsertRowsCommand("nbri_ehr", "Conception"); - conception.addRow(Map.of("ConceptId", conceptId, "ConceptDate", now.minusDays(160), "Dam", "TEST4551032")); + conception.addRow(Map.of("ConceptId", conceptId, "ConceptDate", now.minusDays(160), "Dam", damId, "Sire", sireId)); conception.execute(getApiHelper().getConnection(), getContainerPath()); gotoEnterData(); @@ -622,15 +648,47 @@ public void testBirthForm() throws IOException, CommandException lockForm(); Ext4GridRef births = _helper.getExt4GridForFormSection("Births"); - _helper.addRecordToGrid(births); + verifyBirthColumnOrder(births); + + log("Starting a birth record from the conception"); + births.clickTbarButton("Start with Conception"); + Window conceptionWindow = new Window.WindowFinder(getDriver()).withTitle("Start with Conception").waitFor(); + Ext4ComboRef conceptionCombo = _ext4Helper.queryOne("window #conceptionField", Ext4ComboRef.class); + Assert.assertNotNull("Conception Id field not found in the Start with Conception window", conceptionCombo); + conceptionCombo.waitForStoreLoad(); + conceptionCombo.setComboByDisplayValue(conceptId); + conceptionWindow.clickButton("Submit", 0); + births.waitForRowCount(1); + + log("Verifying the conception populated the new birth record"); + assertEquals("Conception Id was not copied from the conception", conceptId, births.getFieldValue(1, "conceptId")); + assertEquals("Dam was not copied from the conception", damId, births.getFieldValue(1, "Id/demographics/dam")); + assertEquals("Sire was not copied from the conception", sireId, births.getFieldValue(1, "Id/demographics/sire")); + assertEquals("Species was not copied from the dam of the conception", damSpeciesCode, births.getFieldValue(1, "Id/demographics/species")); + + log("Verifying Conception Id is required"); + births.setGridCellJS(1, "conceptId", null); + waitForFormError("The field: Conception Id is required"); + births.setGridCellJS(1, "conceptId", conceptId); + births.setGridCellJS(1, "date", now.minusDays(1).format(DateTimeFormatter.ofPattern(DATE_TIME_FORMAT_STRING))); births.setGridCell(1, "Id", bornAnimal); births.setGridCell(1, "cage", "C3"); - births.setGridCell(1, "Id/demographics/species", "Cebus apella CAP"); - births.setGridCell(1, "Id/demographics/gender", "female"); - births.setGridCell(1, "project", "795644"); - births.setGridCell(1, "birthProtocol", "protocol101"); - births.setGridCell(1, "conceptId", conceptId); + births.setGridCell(1, "Id/demographics/gender", "Female"); + births.setGridCell(1, "breedingType", breedingType); + + Ext4GridRef protocolAssignments = _helper.getExt4GridForFormSection("Protocol Assignment"); + _helper.addRecordToGrid(protocolAssignments); + protocolAssignments.setGridCell(1, "Id", bornAnimal); + protocolAssignments.setGridCellJS(1, "date", now.minusDays(1).format(DateTimeFormatter.ofPattern(DATE_TIME_FORMAT_STRING))); + protocolAssignments.setGridCell(1, "protocol", "protocol101"); + + Ext4GridRef projectAssignments = _helper.getExt4GridForFormSection("Project Assignment"); + _helper.addRecordToGrid(projectAssignments); + projectAssignments.setGridCell(1, "Id", bornAnimal); + projectAssignments.setGridCellJS(1, "date", now.minusDays(1).format(DateTimeFormatter.ofPattern(DATE_TIME_FORMAT_STRING))); + projectAssignments.setGridCell(1, "project", "795644"); + submitForm("Submit Final", "Finalize"); goToSchemaBrowser(); @@ -638,20 +696,39 @@ public void testBirthForm() throws IOException, CommandException table.setFilter("Id", "Equals", bornAnimal); Assert.assertEquals("Invalid Birth record", Arrays.asList(bornAnimal), table.getRowDataAsText(0, "Id")); Assert.assertEquals("Invalid Birth record", Arrays.asList("C3"), table.getRowDataAsText(0, "cage")); - Assert.assertEquals("Invalid Birth record", Arrays.asList("795644"), table.getRowDataAsText(0, "project")); - Assert.assertEquals("Invalid Birth record", Arrays.asList("protocol101"), table.getRowDataAsText(0, "birthProtocol")); Assert.assertEquals("Invalid Birth record", Arrays.asList(conceptId), table.getRowDataAsText(0, "conceptId")); + Assert.assertEquals("Invalid Birth record", Arrays.asList(breedingType), table.getRowDataAsText(0, "breedingType")); + + log("Verifying the dam and sire of the conception reached demographics"); + goToSchemaBrowser(); + table = viewQueryData("study", "demographics"); + table.setFilter("Id", "Equals", bornAnimal); + Assert.assertEquals("Invalid demographics record", Arrays.asList(damId), table.getRowDataAsText(0, "dam")); + Assert.assertEquals("Invalid demographics record", Arrays.asList(sireId), table.getRowDataAsText(0, "sire")); + Assert.assertEquals("Invalid demographics record", Arrays.asList(damSpecies), table.getRowDataAsText(0, "species")); + + goToSchemaBrowser(); + table = viewQueryData("study", "assignment"); + table.setFilter("Id", "Equals", bornAnimal); + Assert.assertEquals("Invalid project assignment", Arrays.asList("795644"), table.getRowDataAsText(0, "project")); + + goToSchemaBrowser(); + table = viewQueryData("study", "protocolAssignment"); + table.setFilter("Id", "Equals", bornAnimal); + Assert.assertEquals("Invalid protocol assignment", Arrays.asList("protocol101"), table.getRowDataAsText(0, "protocol")); verifyRowCreated("study", "assignment", bornAnimal, 1); verifyRowCreated("study", "protocolAssignment", bornAnimal, 1); verifyRowCreated("study", "housing", bornAnimal, 1); verifyRowCreated("study", "demographics", bornAnimal, 1); - log("Verifying conception outcome in ConceptionsByDam"); + log("Verifying conception outcome and offspring in ConceptionsByDam"); goToSchemaBrowser(); DataRegionTable report = viewQueryData("nbri_ehr", "ConceptionsByDam"); report.setFilter("ConceptId", "Equals", conceptId); + Assert.assertEquals("Invalid ConceptionsByDam row", Arrays.asList(damId), report.getRowDataAsText(0, "Id")); Assert.assertEquals("Invalid ConceptionsByDam row", Arrays.asList("Live Birth"), report.getRowDataAsText(0, "conceptionOutcome")); + Assert.assertEquals("Invalid ConceptionsByDam row", Arrays.asList(bornAnimal), report.getRowDataAsText(0, "offspring")); } @Test @@ -706,13 +783,20 @@ public void testConceptionForm() lockForm(); Ext4GridRef conceptions = _helper.getExt4GridForFormSection("Conception"); + Assert.assertFalse("Breeding Type describes the birth and should no longer appear on the Conception form", + conceptions.isColumnPresent("breedingType", false)); + _helper.addRecordToGrid(conceptions); conceptions.setGridCell(1, "ConceptId", conceptId); conceptions.setGridCellJS(1, "ConceptDate", now.minusDays(30).format(_dateFormat)); conceptions.setGridCellJS(1, "ConceptTermDate", now.plusDays(135).format(_dateFormat)); + conceptions.setGridCellJS(1, "Estimated", true); conceptions.setGridCell(1, "Dam", damId); conceptions.setGridCell(1, "Sire", sireId); - conceptions.setGridCell(1, "Remark", "Conception entry test"); + // Remark renders as a textarea, which Ext4GridRef's cell editor helpers cannot drive: they only recognize + // an as the active editor, so the click that opens the textarea is followed by a retry click that + // the open textarea intercepts. Set it through the store instead. + conceptions.setGridCellJS(1, "Remark", "Conception entry test"); submitForm("Submit Final", "Finalize"); goToSchemaBrowser(); @@ -720,6 +804,7 @@ public void testConceptionForm() table.setFilter("ConceptId", "Equals", conceptId); Assert.assertEquals("Invalid Conception record", Arrays.asList(damId), table.getRowDataAsText(0, "Dam")); Assert.assertEquals("Invalid Conception record", Arrays.asList(sireId), table.getRowDataAsText(0, "Sire")); + Assert.assertEquals("Invalid Conception record", Arrays.asList("true"), table.getRowDataAsText(0, "Estimated")); Assert.assertEquals("Invalid Conception record", Arrays.asList("Conception entry test"), table.getRowDataAsText(0, "Remark")); log("Verifying unmatched conception appears as Unknown in ConceptionsByDam"); @@ -1615,6 +1700,44 @@ private int countLines(File file) throws Exception } } + // Creates the parents of a conception. They need a species from the ehr_lookups.species list because the + // Start with Conception window copies the dam's species onto the newborn, and the reference study's + // demographics data carries placeholder species values that no lookup entry matches. + private void createBreedingPair(String damId, String sireId, String species) throws Exception + { + String[] fields = new String[]{"Id", "Species", "Birth", "Gender", "date", "calculated_status", "objectid", "performedby"}; + Object[][] data = new Object[][]{ + {damId, species, (new Date()).toString(), getFemale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}, + {sireId, species, (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", damId + ";" + sireId, Filter.Operator.IN)); + getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), insertCommand, getExtraContext()); + } + + // Asserts the Births columns appear in the expected left to right order. Relative position is checked rather + // than absolute index so that hidden and system columns can come and go without breaking the test. + private void verifyBirthColumnOrder(Ext4GridRef births) + { + List expectedOrder = List.of("Id", "date", "conceptId", "Id/demographics/species", "Id/demographics/gender", + "Id/demographics/dam", "Id/demographics/sire", "cage", "type", "cond", "breedingType", "remark", "performedby"); + + int previousIdx = 0; + String previousCol = null; + for (String col : expectedOrder) + { + int idx = births.getIndexOfColumn(col, true); + Assert.assertTrue("Births column '" + col + "' should appear to the right of '" + previousCol + "'", idx > previousIdx); + previousIdx = idx; + previousCol = col; + } + } + + private void waitForFormError(String message) + { + waitFor(() -> isTextPresent(message), "Form did not report: " + message, WAIT_FOR_JAVASCRIPT); + } + private void verifyRowCreated(String schema, String query, String animalId, int rowCount) { goToSchemaBrowser();