Behavior cases feedback (#434)

* Alopecia workflow
* SIB workflow
* Auto open/close obs orders with cases
* Additional behavior reports
* Behavior rounds form
* Incomplete observations/treatments

nirc_ehr/resources/data/alopecia_score.tsv

@@ -1,25 +1,6 @@
-value	sort_order	description	Date Disabled
-0%	1
-1%	2
-9%	3
-10%	4
-18%	5
-19%	6
-27%	7
-28%	8
-36%	9
-37%	10
-45%	11
-46%	12
-54%	13
-55%	14
-63%	15
-64%	16
-72%	17
-73%	18
-81%	19
-82%	20
-90%	21
-91%	22
-99%	23
-100%	24
+value	title	sort_order	description	Date Disabled
+Very good coat condition (1)	Very good coat condition (1)	1
+1-25% hair loss (2)	1-25% hair loss (2)	2
+25-50% hair loss (3)	25-50% hair loss (3)	3
+More than 50% (4)	More than 50% (4)	4
+Completely bald (5)	Completely bald (5)	5

nirc_ehr/resources/data/bcs_score.tsv

@@ -1,10 +1,10 @@
 value	title	category	description	sort_order	date_disabled
-1	Emaciated
-1.5	Very Thin
-2	Thin
-2.5	Lean
-3	Optimum
-3.5	Slightly Overweight
-4	Heavy
-4.5	Obese
-5	Grossly Obese
+Emaciated (1)				1
+Very Thin (1.5)				2
+Thin (2)				3
+Lean (2.5)				4
+Optimum (3)				5
+Slightly Overweight (3.5)				6
+Heavy (4)				7
+Obese (4.5)				8
+Grossly Obese (5)				9

nirc_ehr/resources/data/behavior_mgmt_codes.tsv

@@ -0,0 +1,4 @@
+value	title	sort_order	description	Date Disabled
+No Fleece Tube	No Fleece Tube	1
+Fleece Tube	Fleece Tube	2
+Wood	Wood	3

nirc_ehr/resources/data/daily_enrich_codes.tsv

@@ -0,0 +1,13 @@
+value	title	sort_order	description	Date Disabled
+Cone	Cone	1
+Cap Feeder	Cap Feeder	2
+Blind Forager	Blind Forager	3
+Dried Fruit	Dried Fruit	4
+Forage on Board	Forage on Board	5
+Forage Tray	Forage Tray	6
+Produce	Produce	7
+Paper Burrito	Paper Burrito	8
+Puzzle Feeder	Puzzle Feeder	9
+Paper	Paper	10
+Fleece Tube Replaced	Fleece Tube Replaced	11
+Other	Other	12

nirc_ehr/resources/data/editable_lookups.tsv

@@ -12,6 +12,7 @@ arrival_type	Colony Management	Arrival Type	Types of arrivals.
 arthritis_types	Clinical	Arthritis Types	Clinical observation fixed values.
 att_score	Behavior	Attitude Score	Behavior observation fixed values.
 bcs_score	Clinical	Body Condition Score	Clinical observation fixed values.
+behavior_mgmt_codes	Behavior	Behavior Managment Codes	Behavior observation fixed values.
 behavior_types	Behavior	Behavior Types	Behavior observation fixed values.
 blood_draw_reason	Clinical	Blood Draw Reason	Used in blood draw datasets.
 blood_draw_tube_type	Clinical	Blood Draw Tube Type	Used in blood draw datasets.
@@ -28,6 +29,7 @@ cost_center	Colony Management	Cost Center
 cost_type	Colony Management	Cost Type
 country	Colony Management	Country
 country_category	Colony Management	Country Category
+daily_enrich_codes	Behavior	Daily enrichment codes.
 data_category	Clinical	Data Categories	Used in datasets.
 death_reason	Colony Management	Death Reason
 delivery_state	Colony Management	Delivery State
@@ -36,6 +38,7 @@ dental_trauma	Clinical	Dental Trauma	Clinical observation fixed values.
 digit_amputation	Clinical	Digit Amputation	Clinical observation fixed values.
 divider_types	Colony Management	Divider Type	Used in cage details.
 dosage_units	Clinical	Dosage Units	Used in drug and treatment datasets.
+drug_defaults	Clinical	Formulary	Default values in drug and treatment datasets.
 ear_types	Clinical	Ear Types	Clinical observation fixed values.
 esig_events	Colony Management	Esig Events
 euthanasia_type	Colony Management	Euthanasia Type
@@ -114,4 +117,6 @@ vendor_production_location	Colony Management	Vendor Production Location
 volume_units	Clinical	Volume Units	Used in drug and treatment datasets.
 weight_ranges	Clinical	Weight Ranges	Min/Max allowable weight per species. Used in various weight reports.
 wound_score	Clinical	Wound Score	Clinical observation fixed values.
-yesno	Clinical	Yes/No Values	Used for yes/no values in various datasets
+wound_severity	Clinical	Wound Severity	Clinical observation fixed values.
+wound_status	Clinical	Wound Status	Clinical observation fixed values.
+yes_no_order	Clinical	Yes/No Values in Order	Used for yes/no values in various datasets. Includes sort order.

nirc_ehr/resources/data/lookup_sets.tsv

@@ -10,6 +10,7 @@ arrival_type	Arrival Type	value
 arthritis_types	Arthritis Types	value
 att_score	Attitude Score	value
 bcs_score	BCS Store	value	title
+behavior_mgmt_codes	Behavior Management Codes	value
 behavior_types	Behavior Types	value
 blood_draw_reason	Blood Draw Reason	value
 blood_sample_type	Blood Sample Types	value
@@ -22,6 +23,7 @@ cost_center	Cost Center	value	title
 cost_type	Cost Type	value	title
 country	Country	value	title
 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_state	Delivery State	value	title
@@ -96,4 +98,6 @@ vendor_approval_code	Vendor Approval Code	value	title
 vendor_production_location	Vendor Production Location	value	title
 weight_ranges	Weight Ranges	value
 wound_score	Wound Score	value
-yesno	Yes/No Values	value
+wound_severity	Wound Severity	value
+wound_status	Wound Status	value
+yes_no_order	Yes/No Values in Order	value

nirc_ehr/resources/data/lookupsManifest.tsv

@@ -12,6 +12,7 @@ arrival_type
 arthritis_types
 att_score
 bcs_score
+behavior_mgmt_codes
 behavior_types
 blood_draw_reason
 blood_draw_tube_type
@@ -25,6 +26,7 @@ conc_units
 cost_type
 country
 country_category
+daily_enrich_codes
 data_category
 death_reason
 delivery_state
@@ -107,4 +109,6 @@ vendor_production_location
 volume_units
 weight_ranges
 wound_score
-yesno
+wound_severity
+wound_status
+yes_no_order

nirc_ehr/resources/data/lookupsManifestTest.tsv

@@ -11,6 +11,7 @@ app_score
 arrival_type
 arthritis_types
 bcs_score
+behavior_mgmt_codes
 behavior_types
 blood_draw_reason
 blood_draw_tube_type
@@ -24,6 +25,7 @@ congenital_abnormalities
 cost_type
 country
 country_category
+daily_enrich_codes
 data_category
 death_reason
 delivery_state
@@ -109,4 +111,6 @@ vendor_production_location
 volume_units
 weight_ranges
 wound_score
-yesno
+wound_severity
+wound_status
+yes_no_order

nirc_ehr/resources/data/observation_types.tsv

@@ -1,7 +1,14 @@
 value	category	editorconfig	schemaName	queryName	valueColumn
-Alopecia Score	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"alopecia_score","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	alopecia_score	value
+Alopecia Score	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"alopecia_score","forceSelection":true,"displayField":"title","valueField":"value","sortFields":"sort_order"}	ehr_lookups	alopecia_score	value
 Alopecia Type	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"alopecia_type","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	alopecia_type	value
 Alopecia Regrowth	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"alopecia_regrowth","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	alopecia_regrowth	value
+Behavior Managment	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"behavior_mgmt_codes","forceSelection":true,"displayField":"title","valueField":"value","sortFields":"sort_order"}	ehr_lookups	behavior_mgmt_codes	value
+Daily Enrichment	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"daily_enrich_codes","forceSelection":true,"displayField":"title","valueField":"value","sortFields":"sort_order"}	ehr_lookups	daily_enrich_codes	value
+Self Biting Observed	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
+New Injury Observed	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
+Other Stereotopy	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
+Environmental Change	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
+Special Enrichment	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
 Preferences	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"preferences","displayField":"value","valueField":"value"}	ehr_lookups	preferences	value
 Temperament	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"temperament","displayField":"value","valueField":"value"}	ehr_lookups	temperament	value
 BCS		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"bcs_score","forceSelection":true,"displayField":"value","valueField":"value"}	ehr_lookups	bcs_score	value
@@ -22,7 +29,7 @@ TB TST Score (Day 2)		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","que
 TB TST Score (Day 3)		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"tb_obs_score","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	tb_obs_score	value
 Auscultation		{"xtype":"textfield"}
 Abdominal Palpation		{"xtype":"textfield"}
-Pregnant		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yesno","forceSelection":true,"displayField":"value","valueField":"value"}	ehr_lookups	yesno	value
+Pregnant		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
 Dental Disease		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"dental_disease","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	dental_disease	value
 Congenital Abnormalities		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"congenital_abnormalities","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	congenital_abnormalities	value
 Urine		{"xtype":"textfield"}
@@ -31,6 +38,8 @@ Gait/Posture		{"xtype":"textfield"}
 Digit Amputation		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"digit_amputation","displayField":"value","valueField":"value"}
 Dental Trauma		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"dental_trauma","displayField":"value","valueField":"value","sortFields":"sort_order"}
 Wound Score		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_score","displayField":"value","valueField":"value","sortFields":"sort_order"}
+Wound Status	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_status","displayField":"value","valueField":"value","sortFields":"sort_order"}
+Wound Severity	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_severity","displayField":"value","valueField":"value","sortFields":"sort_order"}
 Fecal Score		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"fecal_score","displayField":"value","valueField":"value"}	ehr_lookups	fecal_score	value
 Trauma: Laceration		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"trauma_size","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	trauma_size	value
 Trauma: Degloving		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"trauma_size","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	trauma_size	value
@@ -56,6 +65,6 @@ Respiratory Tract		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryN
 Feed Assessment	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"feed_assess_types","displayField":"value","valueField":"value"}	ehr_lookups	feed_assess_types	value
 Stool		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"stool_types","displayField":"value","sortFields":"sort_order","valueField":"value"}
 Activity	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"activity","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	activity	value
-Verified Id?		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yesno","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yesno	value
+Verified Id?		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
 Turgor		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"turgor_score","displayField":"value","sortFields":"sort_order","valueField":"value"}
 SIB Score	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"sib_score","forceSelection":true,"displayField":"value","valueField":"value"}	ehr_lookups	sib_score	value

nirc_ehr/resources/data/treatment_frequency.tsv

@@ -1,5 +1,6 @@
 Meaning	Sort Order	Week of Month	Day of Month	Day of Week	Interval in Days	Short Name	Active?
 Monthly					30		true
+Weekly					7		true
 Alternating Days					2		true
 SID					1		true
 QID					1		true

nirc_ehr/resources/data/treatment_frequency_times.tsv

@@ -1,6 +1,7 @@
 Frequency	Hour of Day	Time Description
 SID	800	AM
 Monthly	800	AM
+Weekly	800	AM
 Alternating Days	800	AM
 TID	800	AM
 TID	1200	PM

nirc_ehr/resources/data/wound_severity.tsv

@@ -0,0 +1,6 @@
+value	sort_order
+N/A (0)	1
+Superficial (1)	2
+Partial Thickness (2)	3
+Full Thickness (3)	4
+Muscle Damage (4)	5

nirc_ehr/resources/data/wound_status.tsv

@@ -0,0 +1,5 @@
+value	sort_order
+Completely Healed (0)	1
+Mostly Healed (1)	2
+Partially Healed (2)	3
+Not Healed (4)	4

nirc_ehr/resources/data/yes_no_order.tsv

@@ -0,0 +1,4 @@
+value	sort_order
+Yes	1
+No	2
+N/A	3

nirc_ehr/resources/queries/ehr_lookups/snomed.query.xml

@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="snomed" tableDbType="TABLE">
+                <tableTitle>Treatments</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>

nirc_ehr/resources/queries/study/cases.js

@@ -24,7 +24,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
         }
 
         var reopen = oldRow && oldRow.enddate && !row.enddate;
-        if (!helper.isValidateOnly() && (reopen || helper.getEvent() == 'insert') && row.caseid && row.Id && row.performedby && row.taskid) {
+        if (!helper.isValidateOnly() && (reopen || helper.getEvent() == 'insert') && row.caseid && row.Id && row.performedby && row.taskid && row.category == 'Clinical') {
             var qc;
             if (row.QCStateLabel) {
                 qc = EHR.Server.Security.getQCStateByLabel(row.QCStateLabel);

nirc_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml

@@ -4,8 +4,7 @@
         <column name="caseHistory"/>
         <column name="Id"/>
         <column name="Id/Demographics/species"/>
-        <column name="Id/curLocation/room/building"/>
-        <column name="Id/curLocation/room"/>
+        <column name="Id/curLocation/cage/room/fullRoom"/>
         <column name="Id/curLocation/cage"/>
         <column name="date"/>
         <column name="reviewdate"/>

nirc_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml

@@ -1,6 +1,7 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView">
     <columns>
         <column name="caseCheck"/>
+        <column name="caseHistory"/>
         <column name="Id"/>
         <column name="Id/curLocation/cage">
             <properties>
@@ -22,10 +23,9 @@
         <column name="openRemark"/>
         <column name="plan"/>
         <column name="closeRemark"/>
-        <column name="caseHistory"/>
     </columns>
     <filters>
-        <filter column="enddate" operator="isblank"/>
+        <filter column="isOpen" operator="eq" value="true"/>
         <filter column="category" operator="eq" value="Clinical"/>
     </filters>
     <sorts>

nirc_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml

@@ -1,17 +1,21 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView">
     <columns>
+        <column name="caseCheck"/>
+        <column name="caseHistory"/>
         <column name="Id"/>
-        <column name="Id/curLocation/room"/>
+        <column name="Id/Demographics/species"/>
+        <column name="Id/curLocation/cage/room/fullRoom"/>
         <column name="Id/curLocation/cage"/>
         <column name="date"/>
         <column name="reviewdate"/>
         <column name="enddate"/>
+        <column name="Id/demographics/mostRecentHx"/>
         <column name="problemCategory"/>
         <column name="problemSubcategory"/>
+        <column name="Id/curLocation/daysInRoom"/>
         <column name="remark"/>
         <column name="plan"/>
-        <column name="caseHistory"/>
-        <column name="taskid"/>
+        <column name="daysSinceLastVetReview"/>
     </columns>
     <filters>
         <filter column="category" operator="eq" value="Behavior"/>

nirc_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml

@@ -1,6 +1,7 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView">
     <columns>
         <column name="caseCheck"/>
+        <column name="caseHistory"/>
         <column name="Id"/>
         <column name="Id/curLocation/cage">
             <properties>

nirc_ehr/resources/queries/study/clinical_observations.js

@@ -27,6 +27,15 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
             EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'No' for 'Verified Id?', please enter Remark", "WARN");
         }
 
+        if (row.category === "Daily Enrichment" && row.observation === "Other" && !row.remark) {
+            EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Other' for 'Daily Enrichment', please enter Remark", "WARN");
+        }
+
+        var yesRemarkRequired = (row.category === "Self Biting Observed" || row.category === "New Injury Observed" || row.category === "Other Stereotopy" || row.category === "Environmental Change" || row.category === "Special Enrichment");
+        if (yesRemarkRequired && row.observation === "Yes" && !row.remark) {
+            EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Yes' for " + row.category + ", please explain in the Remark", "WARN");
+        }
+
         // Handle scheduled observations
         if (!helper.isValidateOnly() && row.scheduledDate) {
             var qc;

nirc_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml

@@ -12,6 +12,6 @@
         <column name="QCState"/>
     </columns>
     <filters>
-        <filter column="category" operator="eq" value="Behavior"/>
+        <filter column="type" operator="eq" value="Behavior"/>
     </filters>
 </customView>

nirc_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml

@@ -0,0 +1,17 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="date" descending="true"/>
+    </sorts>
+    <columns>
+        <column name="Id"/>
+        <column name="date"/>
+        <column name="area"/>
+        <column name="observation"/>
+        <column name="remark"/>
+        <column name="performedBy"/>
+        <column name="QCState"/>
+    </columns>
+    <filters>
+        <filter column="type" operator="eq" value="Clinical"/>
+    </filters>
+</customView>