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6 changes: 6 additions & 0 deletions EHR_App/resources/data/calculated_status_codes.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
code
Alive
Dead
ERROR
No Record
Shipped
2 changes: 2 additions & 0 deletions EHR_App/resources/data/editable_lookups.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
sch query category title description

2 changes: 2 additions & 0 deletions EHR_App/resources/data/lookup_sets.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
setname label keyfield titleColumn

11 changes: 11 additions & 0 deletions EHR_App/resources/data/lookupsManifest.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
name
editable_lookups
areas
buildings
cage
cage_type
calculated_status_codes
gender_codes
rooms
source
species
11 changes: 11 additions & 0 deletions EHR_App/resources/data/lookupsManifestTest.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
name
editable_lookups
areas
buildings
cage
cage_type
calculated_status_codes
gender_codes
rooms
source
species
19 changes: 0 additions & 19 deletions EHR_App/resources/data/reports/reports.tsv

This file was deleted.

34 changes: 34 additions & 0 deletions EHR_App/resources/queries/study/Pedigree.sql
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
/*
* Copyright (c) 2015-2018 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT

d.id as Id,
d.dam as Dam,
d.sire as Sire,

CASE (d.id.demographics.gender.code)
WHEN 'e' THEN 1
WHEN 'm' THEN 1
WHEN 'v' THEN 1
WHEN 'c' THEN 2
WHEN 'f' THEN 2
WHEN 's' THEN 2
ELSE 3
END AS gender,
d.id.demographics.gender.meaning as gender_code,
CASE (d.id.demographics.calculated_status)
WHEN 'Alive' THEN 0
ELSE 1
END
AS status,
d.id.demographics.calculated_status as status_code,
d.id.demographics.species.common as species,
'' as Display,
'Demographics' as source,
d.modified

FROM study.demographics d
WHERE d.Dam IS NOT NULL OR d.Sire IS NOT NULL
25 changes: 25 additions & 0 deletions EHR_App/resources/reports/additionalReports.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
reportname category reporttype reporttitle visible containerpath schemaname queryname viewname report datefieldname todayonly queryhaslocation sort_order QCStateLabelFieldName description supportsNonIdFilters
behaviorRemarks
clinObsBehavior
pairingsBehavior
pairingHousingSummary
pairingHistory
alopecia
biopsy
clinremarks
currentBlood
obs
physicalExam
serology
breeder
exemptions
pairings
bloodSchedule
clinMedicationSchedule
dietSchedule
incompleteTreatments
surgMedicationSchedule
surgMedicationScheduleDaily
inbreeding
necropsy
pregnancy

This file was deleted.

Original file line number Diff line number Diff line change
@@ -1,65 +1,65 @@
objectid Id date birth death calculated_status gender sire dam species origin geographic_origin
1 44444 -1381d -1381d ALIVE 1 44442 44443 171 00001
2 TSTCP -1382d -1382d ALIVE 1 44442 44443 171 00002
3 44446 -1406d -1406d ALIVE 1 44442 44443 171 00003
4 44445 -1414d -1414d -726d DEAD 2 44442 44443 171 00004
5 TEST3844307 -2454d -2454d ALIVE 1 5748235 TEST2312318 171 00005
6 TEST8976544 -2470d -2470d ALIVE 2 9516255 8739374 20 00001 CHINESE
7 TEST9195996 -2473d -2473d ALIVE 1 TEST6390238 TEST2312318 171 00002
8 TEST6208376 -2500d -2500d ALIVE 2 2568235 5961588 20 00003 CHINESE
9 TEST6700530 -2507d -2507d -2132d DEAD 1 9516255 7773678 20 00004 CHINESE
10 TEST3621582 -2759d -2759d ALIVE 2 TEST6390238 TEST2312318 171 00005
11 TEST3224553 -2779d -2779d -2189d DEAD 2 4434585 7877112 20 00001 CHINESE
12 TEST727088 -2815d -2815d ALIVE 2 3686702 9719847 20 00002 CHINESE
13 TEST1112911 -2819d -2819d ALIVE 2 731544 6914348 20 00003 CHINESE
14 TEST1020148 -2908d -2908d -2235d DEAD 2 57307 7166552 171 00004
15 TEST1099252 -2916d -2916d -2244d DEAD 2 TEST6390238 TEST2312318 171 00005
16 TEST1441142 -2918d -2918d -2231d DEAD 2 731544 1256797 20 00001 CHINESE
17 TEST4037096 -2930d -2930d ALIVE 2 4597773 20 00002 CHINESE
18 TEST3771679 -2958d -2958d ALIVE 2 TEST6390238 TEST2312318 171 00003
19 TEST9118022 -2980d -2980d -2262d DEAD 2 2042908 7257197 20 00004 CHINESE
20 TEST5409620 -2989d -2989d ALIVE 1 9468964 6954679 20 00005 CHINESE
21 TEST5131891 -2993d -2993d ALIVE 1 2480492 2001039 20 00001 CHINESE
22 TEST5158984 -3005d -3005d ALIVE 1 TEST6390238 TEST2312318 171 00002
23 TEST7151371 -3022d -3022d ALIVE 1 2042908 838626 20 00003 CHINESE
24 TEST3137998 -3025d -3025d ALIVE 1 4778953 690232 20 00004 CHINESE
25 TEST4945025 -3082d -3082d ALIVE 1 9819418 3066209 20 00005 CHINESE
26 TEST1684145 -3087d -3087d ALIVE 2 4891303 8982969 20 00001 CHINESE
27 TEST5598475 -3091d -3091d ALIVE 1 TEST6390238 TEST2312318 171 00002
28 TEST7407382 -3178d -3178d ALIVE 1 731451 1712704 20 00003 INDIAN
29 TEST8533200 -3209d -3209d ALIVE 1 9468964 1636539 20 00004 INDIAN
30 TEST3843301 -3219d -3219d ALIVE 1 731544 TEST2312318 171 00005
31 TEST4935165 -3240d -3240d ALIVE 2 6974794 4343642 20 00001 INDIAN
32 TEST2227135 -3242d -3242d ALIVE 2 TEST6390238 TEST2312318 171 00002
33 TEST5292692 -3310d -3310d ALIVE 1 5542511 4076261 20 00003 INDIAN
34 TEST4013108 -3334d -3334d ALIVE 1 4891303 7524224 171 00004
35 TEST3935154 -3338d -3338d ALIVE 1 7785547 7579363 171 00005
36 TEST4710248 -3341d -3341d ALIVE 1 9819418 642333 20 00001 INDIAN
37 TEST2950014 -3358d -3358d -2224d DEAD 1 4778953 3386291 20 00002 INDIAN
38 TEST5171727 -3360d -3360d ALIVE 1 731544 116526 20 00003 INDIAN
39 TEST499022 -3566d -3566d ALIVE 2 731451 532430 171 00004
40 TEST2008446 -3618d -3618d ALIVE 2 4884340 7405528 20 00005 INDIAN
41 TEST3997535 -3637d -3637d ALIVE 2 4778953 9681212 20 00001 INDIAN
42 TEST6390238 -3923d -3923d ALIVE 2 3565069 5250080 171 00002
43 TEST4564246 -4622d -4622d ALIVE 2 8296075 7877112 171 00003
44 TEST5904521 -5431d -5431d ALIVE 1 8377984 20 00004 INDIAN
45 TEST3804589 -5806d -5806d ALIVE 1 493957 9749422 20 00005 INDIAN
46 TEST4551032 -6362d -6362d ALIVE 1 5030167 8416939 20 00001 INDIAN
47 TEST2312318 -8069d -8069d ALIVE 1 5748235 8739374 171 00002
48 TEST1993532 -11808d -11808d -2259d DEAD 2 5409336 3784452 20 00003 INDIAN
49 TESTMICE101 -2200d -2200d ALIVE 1 200 00001 INDIAN
50 TESTMICE102 -500d -500d ALIVE 2 TESTMICE101 200 00001
51 TESTRAT101 -1500d -1500d ALIVE 1 300 00002 CHINESE
52 TESTRAT102 -700d -700d ALIVE 2 TESTRAT101 300 00002
53 TESTGPIG101 -1750d -1750d ALIVE 1 400 00003 INDIAN
54 TESTGPIG102 -750d -750d ALIVE 2 TESTGPIG101 400 00003
55 TESTGRBL101 -2275d -2275d ALIVE 1 500 00004 INDIAN
56 TESTGRBL102 -1000d -1000d ALIVE 2 TESTGRBL101 500 00004
57 TESTRBT101 -3100d -3100d ALIVE 1 600 00005 CHINESE
58 TESTRBT102 -500d -500d ALIVE 2 TESTRBT101 600 00005
59 TESTHMSTR101 -1100d -1100d ALIVE 1 700 00001 INDIAN
60 TESTHMSTR102 -375d -375d ALIVE 2 TESTHMSTR101 700 00001
61 TESTCAT101 -2612d -2612d ALIVE 1 800 00002 CHINESE
62 TESTCAT102 -1125d -1125d ALIVE 2 TESTCAT101 800 00002
63 AnimalTx01 -1125d -1125d ALIVE 1 44442 44443 171 00001
64 AnimalTx02 -1125d -1125d ALIVE 2 44442 44443 171 00001
1 44444 -1381d -1381d Alive 1 44442 44443 171 00001
2 TSTCP -1382d -1382d Alive 1 44442 44443 171 00002
3 44446 -1406d -1406d Alive 1 44442 44443 171 00003
4 44445 -1414d -1414d -726d Dead 2 44442 44443 171 00004
5 TEST3844307 -2454d -2454d Alive 1 5748235 TEST2312318 171 00005
6 TEST8976544 -2470d -2470d Alive 2 9516255 8739374 20 00001 CHINESE
7 TEST9195996 -2473d -2473d Alive 1 TEST6390238 TEST2312318 171 00002
8 TEST6208376 -2500d -2500d Alive 2 2568235 5961588 20 00003 CHINESE
9 TEST6700530 -2507d -2507d -2132d Dead 1 9516255 7773678 20 00004 CHINESE
10 TEST3621582 -2759d -2759d Alive 2 TEST6390238 TEST2312318 171 00005
11 TEST3224553 -2779d -2779d -2189d Dead 2 4434585 7877112 20 00001 CHINESE
12 TEST727088 -2815d -2815d Alive 2 3686702 9719847 20 00002 CHINESE
13 TEST1112911 -2819d -2819d Alive 2 731544 6914348 20 00003 CHINESE
14 TEST1020148 -2908d -2908d -2235d Dead 2 57307 7166552 171 00004
15 TEST1099252 -2916d -2916d -2244d Dead 2 TEST6390238 TEST2312318 171 00005
16 TEST1441142 -2918d -2918d -2231d Dead 2 731544 1256797 20 00001 CHINESE
17 TEST4037096 -2930d -2930d Alive 2 4597773 20 00002 CHINESE
18 TEST3771679 -2958d -2958d Alive 2 TEST6390238 TEST2312318 171 00003
19 TEST9118022 -2980d -2980d -2262d Dead 2 2042908 7257197 20 00004 CHINESE
20 TEST5409620 -2989d -2989d Alive 1 9468964 6954679 20 00005 CHINESE
21 TEST5131891 -2993d -2993d Alive 1 2480492 2001039 20 00001 CHINESE
22 TEST5158984 -3005d -3005d Alive 1 TEST6390238 TEST2312318 171 00002
23 TEST7151371 -3022d -3022d Alive 1 2042908 838626 20 00003 CHINESE
24 TEST3137998 -3025d -3025d Alive 1 4778953 690232 20 00004 CHINESE
25 TEST4945025 -3082d -3082d Alive 1 9819418 3066209 20 00005 CHINESE
26 TEST1684145 -3087d -3087d Alive 2 4891303 8982969 20 00001 CHINESE
27 TEST5598475 -3091d -3091d Alive 1 TEST6390238 TEST2312318 171 00002
28 TEST7407382 -3178d -3178d Alive 1 731451 1712704 20 00003 INDIAN
29 TEST8533200 -3209d -3209d Alive 1 9468964 1636539 20 00004 INDIAN
30 TEST3843301 -3219d -3219d Alive 1 731544 TEST2312318 171 00005
31 TEST4935165 -3240d -3240d Alive 2 6974794 4343642 20 00001 INDIAN
32 TEST2227135 -3242d -3242d Alive 2 TEST6390238 TEST2312318 171 00002
33 TEST5292692 -3310d -3310d Alive 1 5542511 4076261 20 00003 INDIAN
34 TEST4013108 -3334d -3334d Alive 1 4891303 7524224 171 00004
35 TEST3935154 -3338d -3338d Alive 1 7785547 7579363 171 00005
36 TEST4710248 -3341d -3341d Alive 1 9819418 642333 20 00001 INDIAN
37 TEST2950014 -3358d -3358d -2224d Dead 1 4778953 3386291 20 00002 INDIAN
38 TEST5171727 -3360d -3360d Alive 1 731544 116526 20 00003 INDIAN
39 TEST499022 -3566d -3566d Alive 2 731451 532430 171 00004
40 TEST2008446 -3618d -3618d Alive 2 4884340 7405528 20 00005 INDIAN
41 TEST3997535 -3637d -3637d Alive 2 4778953 9681212 20 00001 INDIAN
42 TEST6390238 -3923d -3923d Alive 2 3565069 5250080 171 00002
43 TEST4564246 -4622d -4622d Alive 2 8296075 7877112 171 00003
44 TEST5904521 -5431d -5431d Alive 1 8377984 20 00004 INDIAN
45 TEST3804589 -5806d -5806d Alive 1 493957 9749422 20 00005 INDIAN
46 TEST4551032 -6362d -6362d Alive 1 5030167 8416939 20 00001 INDIAN
47 TEST2312318 -8069d -8069d Alive 1 5748235 8739374 171 00002
48 TEST1993532 -11808d -11808d -2259d Dead 2 5409336 3784452 20 00003 INDIAN
49 TESTMICE101 -2200d -2200d Alive 1 200 00001 INDIAN
50 TESTMICE102 -500d -500d Alive 2 TESTMICE101 200 00001
51 TESTRAT101 -1500d -1500d Alive 1 300 00002 CHINESE
52 TESTRAT102 -700d -700d Alive 2 TESTRAT101 300 00002
53 TESTGPIG101 -1750d -1750d Alive 1 400 00003 INDIAN
54 TESTGPIG102 -750d -750d Alive 2 TESTGPIG101 400 00003
55 TESTGRBL101 -2275d -2275d Alive 1 500 00004 INDIAN
56 TESTGRBL102 -1000d -1000d Alive 2 TESTGRBL101 500 00004
57 TESTRBT101 -3100d -3100d Alive 1 600 00005 CHINESE
58 TESTRBT102 -500d -500d Alive 2 TESTRBT101 600 00005
59 TESTHMSTR101 -1100d -1100d Alive 1 700 00001 INDIAN
60 TESTHMSTR102 -375d -375d Alive 2 TESTHMSTR101 700 00001
61 TESTCAT101 -2612d -2612d Alive 1 800 00002 CHINESE
62 TESTCAT102 -1125d -1125d Alive 2 TESTCAT101 800 00002
63 AnimalTx01 -1125d -1125d Alive 1 44442 44443 171 00001
64 AnimalTx02 -1125d -1125d Alive 2 44442 44443 171 00001
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