diff --git a/onprc_ehr/resources/queries/study/IPC_CassetteColors.sql b/onprc_ehr/resources/queries/study/IPC_CassetteColors.sql new file mode 100644 index 000000000..1d8615bbb --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_CassetteColors.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCCassetteColor' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_CassettePrinting.query.xml b/onprc_ehr/resources/queries/study/IPC_CassettePrinting.query.xml new file mode 100644 index 000000000..411c222a9 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_CassettePrinting.query.xml @@ -0,0 +1,87 @@ + + + + + + + IPC Cassette Printing + + + true + + + + Id + + + + Date + + + + Tissue Types + + study + IPC_TissueTypes + value + + + + + PI Label Text + + + + Cassette Color + + study + IPC_CassetteColors + value + + + + + Remarks + + + + + study + qcstate + RowId + + + + + Task Id + + ehr + tasks + taskid + + + + true + + + Performed By + + + true + + + + + true + + + + + true + + + +
+ + + \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_CurrentFixative.sql b/onprc_ehr/resources/queries/study/IPC_CurrentFixative.sql new file mode 100644 index 000000000..938ce4733 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_CurrentFixative.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCCurrentFixative' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_Embedding.sql b/onprc_ehr/resources/queries/study/IPC_Embedding.sql new file mode 100644 index 000000000..c6eaaaf27 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Embedding.sql @@ -0,0 +1,3 @@ +-- Get Embedding values +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCEmbedding' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_FixationMethod.sql b/onprc_ehr/resources/queries/study/IPC_FixationMethod.sql new file mode 100644 index 000000000..6ecbe81c9 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_FixationMethod.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCFixationMethod' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_FrozenSectionThickness.sql b/onprc_ehr/resources/queries/study/IPC_FrozenSectionThickness.sql new file mode 100644 index 000000000..fba375624 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_FrozenSectionThickness.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCFrozenSectionThickness' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_FrozenSectioning.sql b/onprc_ehr/resources/queries/study/IPC_FrozenSectioning.sql new file mode 100644 index 000000000..58c327335 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_FrozenSectioning.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCFrozenSectioning' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_HandE.sql b/onprc_ehr/resources/queries/study/IPC_HandE.sql new file mode 100644 index 000000000..2ce40daf3 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_HandE.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCHAndE' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_IHC.sql b/onprc_ehr/resources/queries/study/IPC_IHC.sql new file mode 100644 index 000000000..ae25fc6a7 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_IHC.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCIHC' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_IHCAntibody.sql b/onprc_ehr/resources/queries/study/IPC_IHCAntibody.sql new file mode 100644 index 000000000..e6c0c0f3f --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_IHCAntibody.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCIHCAntibody' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_Investigators.sql b/onprc_ehr/resources/queries/study/IPC_Investigators.sql new file mode 100644 index 000000000..2daa61cc5 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Investigators.sql @@ -0,0 +1,3 @@ +SELECT lastName + ', ' + firstName as name +From Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.investigators +Where dateDisabled is null diff --git a/onprc_ehr/resources/queries/study/IPC_Locations.sql b/onprc_ehr/resources/queries/study/IPC_Locations.sql new file mode 100644 index 000000000..6841c99bd --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Locations.sql @@ -0,0 +1,3 @@ +SELECT room +From Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.ehr_lookups.rooms +Where dateDisabled is null order by room \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_Other.query.xml b/onprc_ehr/resources/queries/study/IPC_Other.query.xml new file mode 100644 index 000000000..576026f9c --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Other.query.xml @@ -0,0 +1,80 @@ + + + + + + + IPC Other + + + true + + + + Id + + + + Date + + + + Tissue Types + + study + IPC_TissueTypes + value + + + + + Services And Products + + study + IPC_OtherServices + value + + + + + Performed By + + + + + study + qcstate + RowId + + + + + Task Id + + ehr + tasks + taskid + + + + true + + + true + + + + + true + + + + + true + + + +
+ + + \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_OtherServices.sql b/onprc_ehr/resources/queries/study/IPC_OtherServices.sql new file mode 100644 index 000000000..e386f8d10 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_OtherServices.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCOtherServices' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_ParaffinSectioning.sql b/onprc_ehr/resources/queries/study/IPC_ParaffinSectioning.sql new file mode 100644 index 000000000..051c9c60d --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_ParaffinSectioning.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCParaffinSectioning' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_Pathologist.sql b/onprc_ehr/resources/queries/study/IPC_Pathologist.sql new file mode 100644 index 000000000..8aa6bf066 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Pathologist.sql @@ -0,0 +1,3 @@ +SELECT displayname as name +From Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.Reference_StaffNames +Where Type like 'Necropsy' and DisableDate is null diff --git a/onprc_ehr/resources/queries/study/IPC_ProcessingEmbedding.query.xml b/onprc_ehr/resources/queries/study/IPC_ProcessingEmbedding.query.xml new file mode 100644 index 000000000..07d1ee788 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_ProcessingEmbedding.query.xml @@ -0,0 +1,115 @@ + + + + + + + IPC Processing Embedding + + + true + + + + Id + + + + Date + + + + Tissue Types + + study + IPC_TissueTypes + value + + + + + Embedding + + study + IPC_Embedding + value + + + + + Initial Fixative + + study + IPC_FixationMethod + value + + + + + Fixation Duration + + + + Current Fixative + + study + IPC_CurrentFixative + value + + + + + Processing Type + + study + IPC_ProcessingType + value + + + + + Embedding Instructions + + + + Performed By + + + + + study + qcstate + RowId + + + + + Task Id + + ehr + tasks + taskid + + + + true + + + true + + + + + true + + + + + true + + + +
+ + + \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_ProcessingType.sql b/onprc_ehr/resources/queries/study/IPC_ProcessingType.sql new file mode 100644 index 000000000..e83a09e73 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_ProcessingType.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCProcessingType' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_RNAScope.sql b/onprc_ehr/resources/queries/study/IPC_RNAScope.sql new file mode 100644 index 000000000..be4d130ca --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_RNAScope.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCRNAScope' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_SectionThickness.sql b/onprc_ehr/resources/queries/study/IPC_SectionThickness.sql new file mode 100644 index 000000000..c5ee1653e --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_SectionThickness.sql @@ -0,0 +1,2 @@ +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCSectionThickness' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_Sectioning.query.xml b/onprc_ehr/resources/queries/study/IPC_Sectioning.query.xml new file mode 100644 index 000000000..8dbc44715 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Sectioning.query.xml @@ -0,0 +1,102 @@ + + + + + + + IPC Sectioning + + + true + + + + Id + + + + Date + + + + Tissue Types + + study + IPC_TissueTypes + value + + + + + Paraffin Sectioning + + study + IPC_ParaffinSectioning + value + + + + + Paraffin Section Thickness + + study + IPC_SectionThickness + value + + + + + Frozen Section Thickness + + study + IPC_FrozenSectionThickness + value + + + + + Special Instructions + + + + Performed By + + + + + study + qcstate + RowId + + + + + Task Id + + ehr + tasks + taskid + + + + true + + + true + + + + + true + + + + + true + + + +
+ + + \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_ServiceRequestDetails.query.xml b/onprc_ehr/resources/queries/study/IPC_ServiceRequestDetails.query.xml new file mode 100644 index 000000000..566f5ac49 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_ServiceRequestDetails.query.xml @@ -0,0 +1,104 @@ + + + + + + + IPC Service Request Details + + + true + + + + Id + + + + Date + + + + Requested By + + + + Email + + + + Department + + + + Pathologist + + study + IPC_Pathologist + name + + + + + Investigator + + study + IPC_Investigators + name + + + + + Alias + + + + Sample Dropoff/Pickup Location + + study + IPC_Locations + room + + + + + + study + qcstate + RowId + + + + + Task Id + + ehr + tasks + taskid + + + + true + + + Performed By + + + true + + + + + true + + + + + true + + + +
+ + + \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_SlidePrinting.query.xml b/onprc_ehr/resources/queries/study/IPC_SlidePrinting.query.xml new file mode 100644 index 000000000..af5f93e07 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_SlidePrinting.query.xml @@ -0,0 +1,79 @@ + + + + + + + IPC Sectioning + + + true + + + + Id + + + + Date + + + + Tissue Types + + study + IPC_TissueTypes + value + + + + + Project Notes + + + + Additional text on slide + + + + Performed By + + + + + study + qcstate + RowId + + + + + Task Id + + ehr + tasks + taskid + + + + true + + + true + + + + + true + + + + + true + + + +
+ + + \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_Staining.query.xml b/onprc_ehr/resources/queries/study/IPC_Staining.query.xml new file mode 100644 index 000000000..21be6119d --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Staining.query.xml @@ -0,0 +1,124 @@ + + + + + + + IPC Staining + + + true + + + + Id + + + + Date + + + + Tissue Types + + study + IPC_TissueTypes + value + + + + + H And E + + study + IPC_HandE + value + + + + + Special Stain + + study + IPC_Stains + value + + + + + IHC + + study + IPC_IHC + value + + + + + IHC Primary Antibody + + study + IPC_IHCAntibody + value + + + + + Irrevelant Antibody + + + + RNA Scope + + study + IPC_RNAScope + value + + + + + Other + + + + Performed By + + + + + study + qcstate + RowId + + + + + Task Id + + ehr + tasks + taskid + + + + true + + + true + + + + + true + + + + + true + + + +
+ + + \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_Stains.sql b/onprc_ehr/resources/queries/study/IPC_Stains.sql new file mode 100644 index 000000000..d2aa3e2e8 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_Stains.sql @@ -0,0 +1,3 @@ +--Get the stains data +SELECT value, name from Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCStains' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/IPC_TissueTypes.sql b/onprc_ehr/resources/queries/study/IPC_TissueTypes.sql new file mode 100644 index 000000000..028ed41d1 --- /dev/null +++ b/onprc_ehr/resources/queries/study/IPC_TissueTypes.sql @@ -0,0 +1,2 @@ +SELECT value, name From Site.{substitutePath moduleProperty('EHR','EHRStudyContainer')}.onprc_ehr.IPC_Reference_Data +Where name like 'IPCTissueType' and dateDisabled is null \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/Notes_WithLocation.query.xml b/onprc_ehr/resources/queries/study/Notes_WithLocation.query.xml deleted file mode 100644 index 948863812..000000000 --- a/onprc_ehr/resources/queries/study/Notes_WithLocation.query.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - DCM Notes -
- - - diff --git a/onprc_ehr/resources/queries/study/Notes_WithLocation.sql b/onprc_ehr/resources/queries/study/Notes_WithLocation.sql deleted file mode 100644 index 68b54fa60..000000000 --- a/onprc_ehr/resources/queries/study/Notes_WithLocation.sql +++ /dev/null @@ -1,15 +0,0 @@ -Select - Id, - CASE - WHEN id.curLocation.cage is null then id.curLocation.room - ELSE (id.curLocation.room || '-' || id.curLocation.cage) - END AS Location, - date, - actiondate, - enddate, - category, - value, - remark, - qcstate, - taskid -From study.notes \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/TreatmentSchedulePostOps.sql b/onprc_ehr/resources/queries/study/TreatmentSchedulePostOps.sql deleted file mode 100644 index ece5f0b8e..000000000 --- a/onprc_ehr/resources/queries/study/TreatmentSchedulePostOps.sql +++ /dev/null @@ -1,214 +0,0 @@ -/* - * Copyright (c) 2015 LabKey Corporation - * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 - - -- Modified by Kolli on 9/10/2019 -*/ -SELECT - h.id, - h.calculated_status, - --s.TreatmentStatus, - (SELECT max(d.qcstate.label) as label FROM study.drug d WHERE s.objectid = d.treatmentid and s.date = d.timeordered) as TreatmentStatus, - h.Id.curLocation.room as room, - h.Id.curLocation.cage as cage, - s.date, - s.startDate, - s.endDate, - s.dayselapsed, - s.category, - s.code, - s.code.meaning as medication, - s.volume, - s.vol_units, - s.concentration, - s.conc_units, - s.amountWithUnits, - s.amountAndVolume, - s.dosage, - s.dosage_units, - s.frequency, - s.route, - s.reason, - s.remark, - s.performedby -FROM study.demographics h JOIN ( - -SELECT - s.animalid, s.TreatmentStatus, timestampadd('SQL_TSI_MINUTE', ((s.hours * 60) + s.minutes), s.origDate) as date, s.objectid, - s.startdate, s.enddate, s.dayselapsed, s.category, s.code, s.volume, s.vol_units, s.concentration, s.conc_units, - s.amountWithUnits, s.amountAndVolume, s.dosage, s.dosage_units, s.frequency, s.route, s.reason, s.remark, s.performedby -FROM ( - - SELECT - t1.objectid, - t1.id as animalid, - (coalesce(tt.time, ft.hourofday, (hour(t1.date) * 100)) / 100) as hours, - - CASE - WHEN (tt.time IS NOT NULL OR ft.hourofday IS NOT NULL) THEN (((coalesce(tt.time, ft.hourofday) / 100.0) - floor(coalesce(tt.time, ft.hourofday) / 100)) * 100) - ELSE minute(t1.date) - END as minutes, - dr.date as origDate, - - CASE - WHEN snomed.code IS NOT NULL THEN 'Post Op Meds' - ELSE t1.category - END as category, - - t1.date as startDate, - timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly as timestamp), dr.dateOnly) + 1 as daysElapsed, - t1.enddate, t1.code, t1.volume, t1.vol_units, t1.concentration, t1.conc_units, t1.amountWithUnits, - t1.amountAndVolume, t1.dosage, t1.dosage_units, t1.frequency.meaning + ' (' + t1.frequency.times + ')' as frequency, t1.route, - t1.reason, t1.performedby, t1.remark, t1.qcstate.label as TreatmentStatus - - FROM ehr_lookups.dateRange dr - -Join study."Treatment Orders" t1 - ON (dr.dateOnly >= t1.dateOnly and dr.dateOnly <= t1.enddateCoalesced AND - mod(CAST(timestampdiff('SQL_TSI_DAY', CAST(t1.dateOnly as timestamp), dr.dateOnly) as integer), t1.frequency.intervalindays) = 0 - ) - -LEFT JOIN ehr.treatment_times tt ON (tt.treatmentid = t1.objectid) -LEFT JOIN ehr_lookups.treatment_frequency_times ft ON (ft.frequency = t1.frequency.meaning AND tt.rowid IS NULL) - -INNER JOIN ( - SELECT - sc.code - FROM ehr_lookups.snomed_subset_codes sc - WHERE sc.primaryCategory = 'Post Op Meds' - /* Added this clause by Kollil on 10/4/2023 to exclude the MPA injection from the list. - This change is made according to the new request by Cassie Tkt# 9939. The MPA med is part of the post op meds category - but a separate alert is created so, excluding this med from this alert list. - */ - AND sc.code NOT IN ('E-85760') - GROUP BY sc.code -) snomed ON snomed.code = t1.code - ---NOTE: if we run this report on a future interval, we want to include those treatments -WHERE t1.date is not null ---NOTE: they have decided to include non-public data - -) s - -) s ON (s.animalid = h.id) - WHERE h.calculated_status = 'Alive' - --account for date/time in schedule - and s.date >= s.startDate and s.date <= s.enddate - - --- /* --- * Copyright (c) 2015 LabKey Corporation --- * --- * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 --- */ --- --- SELECT --- h.id, --- h.calculated_status, --- s.*, --- s.objectid as treatmentid, --- ---Modified 7-2-2015 Blasa from d.qcstate to d.qcstate.label --- (SELECT max(d.qcstate.label) as label FROM study.drug d WHERE s.objectid = d.treatmentid AND s.date = d.timeordered) as treatmentStatus --- --- --- FROM study.demographics h JOIN ( --- --- SELECT --- s.*, --- timestampadd('SQL_TSI_MINUTE', ((s.hours * 60) + s.minutes), s.origDate) as date, --- CASE --- WHEN (hours >= 6 AND hours < 20) THEN 'AM' --- WHEN (hours < 6 OR hours >= 20) THEN 'PM' --- ELSE 'Other' --- END as timeOfDay, --- --- ((s.hours * 60) + s.minutes) as timeOffset --- --- FROM ( --- --- SELECT --- t1.lsid, --- t1.objectid, --- t1.dataset, --- t1.id as animalid, --- --- coalesce(tt.time, ft.hourofday, ((hour(t1.date) * 100) + minute(t1.date))) as time, --- (coalesce(tt.time, ft.hourofday, (hour(t1.date) * 100)) / 100) as hours, --- CASE --- WHEN (tt.time IS NOT NULL OR ft.hourofday IS NOT NULL) THEN (((coalesce(tt.time, ft.hourofday) / 100.0) - floor(coalesce(tt.time, ft.hourofday) / 100)) * 100) --- ELSE minute(t1.date) --- END as minutes, --- dr.date as origDate, --- --ft.timedescription as timeOfDay, --- CASE --- WHEN (tt.time IS NULL) THEN 'Default' --- ELSE 'Custom' --- END as timeType, --- --- CASE --- WHEN snomed.code IS NOT NULL THEN 'Post Op Meds' --- ELSE t1.category --- END as category, --- --t1.category, --- --- t1.frequency.meaning as frequency, --- t1.date as startDate, --- timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly as timestamp), dr.dateOnly) + 1 as daysElapsed, --- t1.enddate, --- --t1.duration, --- t1.project, --- t1.code, --- --- t1.volume, --- t1.vol_units, --- t1.concentration, --- t1.conc_units, --- t1.amount, --- t1.amount_units, --- t1.amountWithUnits, --- t1.amountAndVolume, --- t1.dosage, --- t1.dosage_units, --- t1.qualifier, --- --- t1.route, --- t1.reason, --- t1.performedby, --- t1.remark, --- --t1.description, --- --- t1.qcstate --- --- FROM ehr_lookups.dateRange dr --- --- JOIN study."Treatment Orders" t1 --- --NOTE: should the enddate consider date/time? --- ON (dr.dateOnly >= t1.dateOnly and dr.dateOnly <= t1.enddateCoalesced AND --- --technically the first day of the treatment is day 1, not day 0 --- mod(CAST(timestampdiff('SQL_TSI_DAY', CAST(t1.dateOnly as timestamp), dr.dateOnly) as integer), t1.frequency.intervalindays) = 0 --- ) --- --- LEFT JOIN ehr.treatment_times tt ON (tt.treatmentid = t1.objectid) --- LEFT JOIN ehr_lookups.treatment_frequency_times ft ON (ft.frequency = t1.frequency.meaning AND tt.rowid IS NULL) --- --- INNER JOIN ( --- SELECT --- sc.code --- from ehr_lookups.snomed_subset_codes sc --- WHERE sc.primaryCategory = 'Post Op Meds' --- GROUP BY sc.code --- ) snomed ON snomed.code = t1.code --- --- --NOTE: if we run this report on a future interval, we want to include those treatments --- WHERE t1.date is not null --- --NOTE: they have decided to include non-public data --- --AND t1.qcstate.publicdata = true --and t1.dateOnly <= curdate() --- --- ) s --- --- ) s ON (s.animalid = h.id) --- --- WHERE h.calculated_status = 'Alive' --- --- --account for date/time in schedule --- and s.date >= s.startDate and s.date <= s.enddate \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/demographicsAssignedVet.query.xml b/onprc_ehr/resources/queries/study/demographicsAssignedVet.query.xml deleted file mode 100644 index 16a065547..000000000 --- a/onprc_ehr/resources/queries/study/demographicsAssignedVet.query.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - Assigned Vets - - - true - - -
- - - - diff --git a/onprc_ehr/resources/queries/study/demographicsAssignedVet.sql b/onprc_ehr/resources/queries/study/demographicsAssignedVet.sql deleted file mode 100644 index 3a7ba2602..000000000 --- a/onprc_ehr/resources/queries/study/demographicsAssignedVet.sql +++ /dev/null @@ -1,58 +0,0 @@ -/* -study.demographicsAssignedVet - -Returns one or more assigned vets per animal ID - * When there is an open case, it returns one record for each vet having an open - case for that animal - * When there is not an open case, it returns one record for the lowest-numbered - matched rule - * VAF2 determines the lowest matched rule for each animal. Doing an inner join - with VAF1 results in only those records matching the lowest matched rule per - animal. The select distinct limits it to a single record. - -Future enhancements - * Add ProjectType to select statement and hide in XML - * Add Protocol_PI to study.vet_assignmentFilter and to onprc_ehr.vet_assignment - * Add species to study.vet_assignmentFilter and to onprc_ehr.vet_assignment - * Add validation to onprc_ehr.vet_assignment to prevent creating a rule that has - * no match in the filter - */ - -SELECT DISTINCT VAF1.Id - , VAF1.AssignedVet - , VAF1.AssignmentType - , VAF1.Room - , VAF1.Area - , VAF1.Calculated_Status - , VAF1.MatchedRule -FROM vetAssignment_filter AS VAF1 - INNER JOIN ( - SELECT VAF2.Id - , MIN(VAF2.matchedRule) AS minRule - FROM vetAssignment_filter AS VAF2 - GROUP BY VAF2.id -) AS VAF3 - ON VAF1.id = VAF3.id - AND VAF1.matchedRule = VAF3.minRule - - --- SELECT VAF1.Id --- , VAF1.AssignedVet --- , VAF1.AssignmentType --- /* , VAF1.AssignmentType AS codeAssignmentType*/ --- , VAF1.Room --- , VAF1.Area --- , VAF1.Project --- , VAF1.Protocol --- , VAF1.ProtocolPI --- , VAF1.Calculated_Status --- , VAF1.MatchedRule --- , VAF1.history --- FROM vetAssignment_filter AS VAF1 --- INNER JOIN ( --- SELECT VAF2.Id --- , MIN(VAF2.matchedRule) AS minRule --- FROM vetAssignment_filter AS VAF2 --- GROUP BY VAF2.id --- ) AS VAF3 ON VAF1.id = VAF3.id --- AND VAF1.matchedRule = VAF3.minRule diff --git a/onprc_ehr/resources/queries/study/treatmentScheduleMPA.query.xml b/onprc_ehr/resources/queries/study/treatmentScheduleMPA.query.xml deleted file mode 100644 index 830f79524..000000000 --- a/onprc_ehr/resources/queries/study/treatmentScheduleMPA.query.xml +++ /dev/null @@ -1,14 +0,0 @@ - - - - - MPA Injections - - - Status - - -
- - - diff --git a/onprc_ehr/resources/queries/study/treatmentScheduleMPA.sql b/onprc_ehr/resources/queries/study/treatmentScheduleMPA.sql deleted file mode 100644 index 13defec33..000000000 --- a/onprc_ehr/resources/queries/study/treatmentScheduleMPA.sql +++ /dev/null @@ -1,98 +0,0 @@ -/* - * Copyright (c) 2015 LabKey Corporation - * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 - - -- Created by Kollil on 9/25/2023 - Tkt# 9939 - Creating a new alert for this medication. This MPA injection is a post op med category but scheduled once a month. - - */ -SELECT - h.id, - h.calculated_status, - --s.TreatmentStatus, - (SELECT max(d.qcstate.label) as label FROM study.drug d WHERE s.objectid = d.treatmentid and s.date = d.timeordered) as TreatmentStatus, - h.Id.curLocation.room as room, - h.Id.curLocation.cage as cage, - s.date, - s.startDate, - s.endDate, - s.dayselapsed, - s.category, - s.code, - s.code.meaning as medication, - s.volume, - s.vol_units, - s.concentration, - s.conc_units, - s.amountWithUnits, - s.amountAndVolume, - s.dosage, - s.dosage_units, - s.frequency, - s.route, - s.reason, - s.remark, - s.performedby -FROM study.demographics h JOIN ( - - SELECT - s.animalid, s.TreatmentStatus, timestampadd('SQL_TSI_MINUTE', ((s.hours * 60) + s.minutes), s.origDate) as date, s.objectid, - s.startdate, s.enddate, s.dayselapsed, s.category, s.code, s.volume, s.vol_units, s.concentration, s.conc_units, - s.amountWithUnits, s.amountAndVolume, s.dosage, s.dosage_units, s.frequency, s.route, s.reason, s.remark, s.performedby - FROM ( - - SELECT - t1.objectid, - t1.id as animalid, - (coalesce(tt.time, ft.hourofday, (hour(t1.date) * 100)) / 100) as hours, - - CASE - WHEN (tt.time IS NOT NULL OR ft.hourofday IS NOT NULL) THEN (((coalesce(tt.time, ft.hourofday) / 100.0) - floor(coalesce(tt.time, ft.hourofday) / 100)) * 100) - ELSE minute(t1.date) - END as minutes, - dr.date as origDate, - - CASE - WHEN snomed.code IS NOT NULL THEN 'Post Op Meds' - ELSE t1.category - END as category, - - t1.date as startDate, - timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly as timestamp), dr.dateOnly) + 1 as daysElapsed, - t1.enddate, t1.code, t1.volume, t1.vol_units, t1.concentration, t1.conc_units, t1.amountWithUnits, - t1.amountAndVolume, t1.dosage, t1.dosage_units, t1.frequency.meaning + ' (' + t1.frequency.times + ')' as frequency, t1.route, - t1.reason, t1.performedby, t1.remark, t1.qcstate.label as TreatmentStatus - - FROM ehr_lookups.dateRange dr - - Join study."Treatment Orders" t1 - ON (dr.dateOnly >= t1.dateOnly and dr.dateOnly <= t1.enddateCoalesced AND - mod(CAST(timestampdiff('SQL_TSI_DAY', CAST(t1.dateOnly as timestamp), dr.dateOnly) as integer), t1.frequency.intervalindays) = 0 - ) - - LEFT JOIN ehr.treatment_times tt ON (tt.treatmentid = t1.objectid) - LEFT JOIN ehr_lookups.treatment_frequency_times ft ON (ft.frequency = t1.frequency.meaning AND tt.rowid IS NULL) - - INNER JOIN ( - SELECT - sc.code - FROM ehr_lookups.snomed_subset_codes sc - WHERE sc.primaryCategory = 'Post Op Meds' - /* Added this clause by Kollil on 10/4/2023 to exclude the MPA injection from the list. - This change is made according to the new request by Cassie Tkt# 9939. The MPA med is part of the post op meds category - so, excluding the other post op meds from this alert list. This list produces only the MPA injection entires. - */ - AND sc.code IN ('E-85760') - GROUP BY sc.code - ) snomed ON snomed.code = t1.code - ---NOTE: if we run this report on a future interval, we want to include those treatments - WHERE t1.date is not null ---NOTE: they have decided to include non-public data - ) s - -) s ON (s.animalid = h.id) -WHERE h.calculated_status = 'Alive' - --account for date/time in schedule - and s.date >= s.startDate and s.date <= s.enddate \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/vetAssignment_demographics.sql b/onprc_ehr/resources/queries/study/vetAssignment_demographics.sql deleted file mode 100644 index 0adf50eb4..000000000 --- a/onprc_ehr/resources/queries/study/vetAssignment_demographics.sql +++ /dev/null @@ -1,92 +0,0 @@ -/* -study.vetAssignment_demographics - -Replaces: study.vetAssignmentDemographics - -Returns at least one record for all living NHPs at the center. -Notes: - * Multiple open cases and multiple assignments for a single animal - result in open cases * assignments for that animal - * Left joins are needed for CMUcases and assignedProject as those tables - might not have records for an animal ID. Left joins are used for all - other joins to be resiliant against missing data. - * enddate.TimeCoalesced is never in the future - -Future modifications: - * Limit open cases to those that are not inactive after confirming w/ Heather - */ - -SELECT demographics.id - , CMUcases.assignedVet.displayName AS caseVet - , CMUcases.date AS caseDate - , housing.room - , housing.room.area - , assignedProject.project AS project - , assignedProject.Protocol AS protocol - , assignedProject.PI AS protocolPI - , assignedProject.projectType AS assignmentType - , demographics.calculated_status - , demographics.gender - , demographics.species - , demographics.history -FROM Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.animal AS nhp -LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.ClinicalCases_Open AS CMUcases -ON CMUcases.id = nhp.id - LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.housing AS housing - ON housing.id = nhp.id - LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.demographics AS demographics - ON demographics.id = nhp.id - LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.vetAssignment_projects AS assignedProject - ON assignedProject.id = nhp.id -WHERE demographics.Calculated_Status = 'Alive' - AND nhp.id NOT LIKE '[A-Z]%' - AND housing.enddate IS NULL - - -/* -study.vetAssignment_demographics.sql - -Replaces: study.vetAssignmentDemographics - -Returns at least one record for all living NHPs at the center. -Notes: - * Multiple open cases and multiple assignments for a single animal - result in open cases * assignments for that animal - * Left joins are needed for CMUcases and assignedProject as those tables - might not have records for an animal ID. Left joins are used for all - other joins to be resiliant against missing data. - -Future modifications: - * Limit open cases to those that are not inactive - */ -/* -SELECT demographics.id - , CMUcases.assignedVet.displayName AS caseVet - , CMUcases.DATE AS caseDate - , housing.room - , housing.room.area - , assignedProject.project AS project - , assignedProject.Protocol AS protocol - , assignedProject.PI AS protocolPI - , assignedProject.projectType AS assignmentType - , demographics.calculated_status - , demographics.gender - , demographics.species - , demographics.history -FROM Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.animal AS nhp -LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.ClinicalCases_Open AS CMUcases -ON CMUcases.id = nhp.id - LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.housing AS housing - ON housing.id = nhp.id - LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.demographics AS demographics - ON demographics.id = nhp.id - LEFT JOIN Site.{ substitutePath moduleProperty('EHR', 'EHRStudyContainer') }.study.vetAssignment_projects AS assignedProject - ON assignedProject.id = nhp.id -WHERE demographics.Calculated_Status = 'Alive' - AND nhp.id NOT LIKE '[A-Z]%' - AND ( - housing.enddateTimeCoalesced >= Curdate() - OR housing.enddateTimeCoalesced IS NULL - ) - -*/ diff --git a/onprc_ehr/resources/queries/study/vetAssignment_projects.sql b/onprc_ehr/resources/queries/study/vetAssignment_projects.sql deleted file mode 100644 index e03256a34..000000000 --- a/onprc_ehr/resources/queries/study/vetAssignment_projects.sql +++ /dev/null @@ -1,70 +0,0 @@ -/* -study.vetAssignment_projects - -Replaces: - * study.vetAssignedResearch - * study.vetAssignedResearch_project - * study.vetAssignedResource - * study.vetAssignedResource_project - -Returns a record for each active assignment of an animal ID to a project. -Notes: - * Animals assigned to multiple projects results in multiple records - * Animals solely on the P51 are not considered "assigned" in PRIMe - and won't have records returned by this query - * Uses Curdate() to avoid issues where an assignment ends on the day this - query is run - * Returns the actual use category instead of "Project Resource Assigned" - or "Project Research Assigned" - */ - -SELECT Id - , project - , project.protocol.external_id AS Protocol - , project.protocol.investigatorID.lastname AS PI - , date - , enddate - , project.use_category AS projectType -FROM study.assignment -WHERE date <= Curdate() - AND ( - enddate IS NULL - OR enddate >= Curdate() - ) - -/* -study.vetAssignment_projects.sql - -Replaces: - * study.vetAssignedResearch - * study.vetAssignedResearch_project - * study.vetAssignedResource - * study.vetAssignedResource_project - -Returns a record for each active assignment of an animal ID to a project. -Notes: - * Animals assigned to multiple projects results in multiple records - * Animals solely on the P51 are not considered "assigned" in PRIMe - and won't have records returned by this query - * Uses Curdate() to avoid issues where an assignment ends on the day this - query is run - * Returns the actual use category instead of "Project Resource Assigned" - or "Project Research Assigned" - */ - -/* -SELECT Id - , project - , project.protocol.external_id AS Protocol - , project.protocol.investigatorID.lastname AS PI - , date - , enddate - , project.use_category AS projectType -FROM study.assignment -WHERE date <= Curdate() - AND ( - enddate IS NULL - OR enddate >= Curdate() - ) - - */ \ No newline at end of file diff --git a/onprc_ehr/resources/queries/study/vetassignment_filter.sql b/onprc_ehr/resources/queries/study/vetassignment_filter.sql deleted file mode 100644 index b0d1ce126..000000000 --- a/onprc_ehr/resources/queries/study/vetassignment_filter.sql +++ /dev/null @@ -1,144 +0,0 @@ -/* -study.vetAssignment_filter - -Partially replaces: study.demographicsAssignedVet, which still exists - -Returns a record for each input record from study.vetAssignment_demographics -using vet assignment rules defined in onprc_ehr.vet_assignment - -Notes: - * This can result in multiple assignments per animal - * Comparisons against rules check for both matches against rule requirements and - no additional rule requirements to ensure no false positives - * Comparisons rely on empty data to be NULL, not "" - * The code prioritizes research projects over non-research projects *for - the same rule* - * Unassigned animals can be found by filtering for "unassigned" in - the AssignedVet column - */ - -SELECT * -FROM ( - SELECT d.Id - , CASE - WHEN d.CaseVet IS NOT NULL THEN d.CaseVet - WHEN R01.UserID IS NOT NULL THEN R01.UserID.DisplayName - WHEN R02.UserID IS NOT NULL THEN R02.UserID.DisplayName - WHEN R03.UserID IS NOT NULL THEN R03.UserID.DisplayName - WHEN R04.UserID IS NOT NULL THEN R04.UserID.DisplayName - WHEN R05.UserID IS NOT NULL THEN R05.UserID.DisplayName - WHEN R06.UserID IS NOT NULL THEN R06.UserID.DisplayName - WHEN R07.UserID IS NOT NULL THEN R07.UserID.DisplayName - WHEN R08.UserID IS NOT NULL THEN R08.UserID.DisplayName - WHEN R09.UserID IS NOT NULL THEN R09.UserID.DisplayName - WHEN R10.UserID IS NOT NULL THEN R10.UserID.DisplayName - WHEN R11.UserID IS NOT NULL THEN R11.UserID.DisplayName - WHEN R12.UserID IS NOT NULL THEN R12.UserID.DisplayName - WHEN R13.UserID IS NOT NULL THEN R13.UserID.DisplayName - WHEN R14.UserID IS NOT NULL THEN R14.UserID.DisplayName - WHEN R15.UserID IS NOT NULL THEN R15.UserID.DisplayName - WHEN R16.UserID IS NOT NULL THEN R16.UserID.DisplayName - WHEN R17.UserID IS NOT NULL THEN R17.UserID.DisplayName - WHEN R18.UserID IS NOT NULL THEN R18.UserID.DisplayName - WHEN R19.UserID IS NOT NULL THEN R19.UserID.DisplayName - WHEN R20.UserID IS NOT NULL THEN R20.UserID.DisplayName - WHEN R21.UserID IS NOT NULL THEN R21.UserID.DisplayName - WHEN R22.UserID IS NOT NULL THEN R22.UserID.DisplayName - ELSE 'Unassigned' - END AS AssignedVet - , CASE - WHEN d.CaseVet IS NOT NULL THEN 'Open Case' - WHEN R01.UserID IS NOT NULL THEN 'Room Priority' - WHEN R02.UserID IS NOT NULL THEN 'Area Priority' - WHEN R03.UserID IS NOT NULL THEN 'Project Room Research Priority' - WHEN R04.UserID IS NOT NULL THEN 'Project Room Resource Priority' - WHEN R05.UserID IS NOT NULL THEN 'Project Room Research' - WHEN R06.UserID IS NOT NULL THEN 'Project Room Resource' - WHEN R07.UserID IS NOT NULL THEN 'Project Area Research Priority' - WHEN R08.UserID IS NOT NULL THEN 'Project Area Resource Priority' - WHEN R09.UserID IS NOT NULL THEN 'Project Area Research' - WHEN R10.UserID IS NOT NULL THEN 'Project Area Resource' - WHEN R11.UserID IS NOT NULL THEN 'Project Research Priority' - WHEN R12.UserID IS NOT NULL THEN 'Project Resource Priority' - WHEN R13.UserID IS NOT NULL THEN 'Project Research' - WHEN R14.UserID IS NOT NULL THEN 'Project Resource' - WHEN R15.UserID IS NOT NULL THEN 'Protocol Room Priority' - WHEN R16.UserID IS NOT NULL THEN 'Protocol Area Priority' - WHEN R17.UserID IS NOT NULL THEN 'Protocol Room' - WHEN R18.UserID IS NOT NULL THEN 'Protocol Area' - WHEN R19.UserID IS NOT NULL THEN 'Protocol Priority' - WHEN R20.UserID IS NOT NULL THEN 'Protocol' - WHEN R21.UserID IS NOT NULL THEN 'Room' - WHEN R22.UserID IS NOT NULL THEN 'Area' - ELSE 'No Matching Rule' - END AS AssignmentType - , d.CaseVet - , d.CaseDate - , d.Project - , d.AssignmentType AS ProjectType - , d.Protocol - , d.ProtocolPI - , d.Room - , d.Area - , d.Calculated_status - , CASE - WHEN d.CaseVet IS NOT NULL THEN 0 - WHEN R01.UserID IS NOT NULL THEN 1 - WHEN R02.UserID IS NOT NULL THEN 2 - WHEN R03.UserID IS NOT NULL THEN 3 - WHEN R04.UserID IS NOT NULL THEN 4 - WHEN R05.UserID IS NOT NULL THEN 5 - WHEN R06.UserID IS NOT NULL THEN 6 - WHEN R07.UserID IS NOT NULL THEN 7 - WHEN R08.UserID IS NOT NULL THEN 8 - WHEN R09.UserID IS NOT NULL THEN 9 - WHEN R10.UserID IS NOT NULL THEN 10 - WHEN R11.UserID IS NOT NULL THEN 11 - WHEN R12.UserID IS NOT NULL THEN 12 - WHEN R13.UserID IS NOT NULL THEN 13 - WHEN R14.UserID IS NOT NULL THEN 14 - WHEN R15.UserID IS NOT NULL THEN 15 - WHEN R16.UserID IS NOT NULL THEN 16 - WHEN R17.UserID IS NOT NULL THEN 17 - WHEN R18.UserID IS NOT NULL THEN 18 - WHEN R19.UserID IS NOT NULL THEN 19 - WHEN R20.UserID IS NOT NULL THEN 20 - WHEN R21.UserID IS NOT NULL THEN 21 - WHEN R22.UserID IS NOT NULL THEN 22 - ELSE 99 - END AS MatchedRule - FROM study.vetAssignment_demographics AS d -/* R01 Room Priority */ LEFT JOIN onprc_ehr.vet_assignment R01 ON (R01.Room = d.Room AND R01.Area IS NULL AND R01.Project IS NULL AND R01.Protocol IS NULL AND R01.Priority = true) -/* R02 Area Priority */ LEFT JOIN onprc_ehr.vet_assignment R02 ON (R02.Area = d.Area AND R02.Room IS NULL AND R02.Project IS NULL AND R02.Protocol IS NULL AND R02.Priority = true) - -/* R03 Project Room Research Priority */ LEFT JOIN onprc_ehr.vet_assignment R03 ON (R03.Project = d.Project AND R03.Room = d.Room AND R03.Area IS NULL AND R03.Protocol IS NULL AND R03.Priority = true AND d.AssignmentType = 'Research') -/* R04 Project Room Resource Priority */ LEFT JOIN onprc_ehr.vet_assignment R04 ON (R04.Project = d.Project AND R04.Room = d.Room AND R04.Area IS NULL AND R04.Protocol IS NULL AND R04.Priority = true AND d.AssignmentType <> 'Research') - -/* R05 Project Room Research */ LEFT JOIN onprc_ehr.vet_assignment R05 ON (R05.Project = d.Project AND R05.Room = d.Room AND R05.Area IS NULL AND R05.Protocol IS NULL AND R05.Priority = false AND d.AssignmentType = 'Research') -/* R06 Project Room Resource */ LEFT JOIN onprc_ehr.vet_assignment R06 ON (R06.Project = d.Project AND R06.Room = d.Room AND R06.Area IS NULL AND R06.Protocol IS NULL AND R06.Priority = false AND d.AssignmentType <> 'Research') - -/* R07 Project Area Research Priority */ LEFT JOIN onprc_ehr.vet_assignment R07 ON (R07.Project = d.Project AND R07.Area = d.Area AND R07.Room IS NULL AND R07.Protocol IS NULL AND R07.Priority = true AND d.AssignmentType = 'Research') -/* R08 Project Area Resource Priority */ LEFT JOIN onprc_ehr.vet_assignment R08 ON (R08.Project = d.Project AND R08.Area = d.Area AND R08.Room IS NULL AND R08.Protocol IS NULL AND R08.Priority = true AND d.AssignmentType <> 'Research') - -/* R09 Project Area Research */ LEFT JOIN onprc_ehr.vet_assignment R09 ON (R09.Project = d.Project AND R09.Area = d.Area AND R09.Room IS NULL AND R09.Protocol IS NULL AND R09.Priority = false AND d.AssignmentType = 'Research') -/* R10 Project Area Resource */ LEFT JOIN onprc_ehr.vet_assignment R10 ON (R10.Project = d.Project AND R10.Area = d.Area AND R10.Room IS NULL AND R10.Protocol IS NULL AND R10.Priority = false AND d.AssignmentType <> 'Research') - -/* R11 Project Research Priority */ LEFT JOIN onprc_ehr.vet_assignment R11 ON (R11.Project = d.Project AND R11.Area IS NULL AND R11.Room IS NULL AND R11.Protocol IS NULL AND R11.Priority = true AND d.AssignmentType = 'Research') -/* R12 Project Resource Priority */ LEFT JOIN onprc_ehr.vet_assignment R12 ON (R12.Project = d.Project AND R12.Area IS NULL AND R12.Room IS NULL AND R12.Protocol IS NULL AND R12.Priority = true AND d.AssignmentType <> 'Research') - -/* R13 Project Research */ LEFT JOIN onprc_ehr.vet_assignment R13 ON (R13.Project = d.Project AND R13.Area IS NULL AND R13.Room IS NULL AND R13.Protocol IS NULL AND R13.Priority = false AND d.AssignmentType = 'Research') -/* R14 Project Resource */ LEFT JOIN onprc_ehr.vet_assignment R14 ON (R14.Project = d.Project AND R14.Area IS NULL AND R14.Room IS NULL AND R14.Protocol IS NULL AND R14.Priority = false AND d.AssignmentType <> 'Research') - -/* R15 Protocol Room Priority */ LEFT JOIN onprc_ehr.vet_assignment R15 ON (R15.Protocol.DisplayName = d.Protocol AND R15.Room = d.Room AND R15.Area IS NULL AND R15.Project IS NULL AND R15.Priority = true) -/* R16 Protocol Area Priority */ LEFT JOIN onprc_ehr.vet_assignment R16 ON (R16.Protocol.DisplayName = d.Protocol AND R16.Area = d.Area AND R16.Room IS NULL AND R16.Project IS NULL AND R16.Priority = true) - -/* R17 Protocol Room */ LEFT JOIN onprc_ehr.vet_assignment R17 ON (R17.Protocol.DisplayName = d.Protocol AND R17.Room = d.Room AND R17.Area IS NULL AND R17.Project IS NULL AND R17.Priority = false) -/* R18 Protocol Area */ LEFT JOIN onprc_ehr.vet_assignment R18 ON (R18.Protocol.DisplayName = d.Protocol AND R18.Area = d.Area AND R18.Room IS NULL AND R18.Project IS NULL AND R18.Priority = false) - -/* R19 Protocol Priority */ LEFT JOIN onprc_ehr.vet_assignment R19 ON (R19.Protocol.DisplayName = d.Protocol AND R19.Area IS NULL AND R19.Room IS NULL AND R19.Project IS NULL AND R19.Priority = true) -/* R20 Protocol */ LEFT JOIN onprc_ehr.vet_assignment R20 ON (R20.Protocol.DisplayName = d.Protocol AND R20.Area IS NULL AND R20.Room IS NULL AND R20.Project IS NULL AND R20.Priority = false) - -/* R21 Room */ LEFT JOIN onprc_ehr.vet_assignment R21 ON (R21.Room = d.Room AND R21.Area IS NULL AND R21.Protocol IS NULL AND R21.Project IS NULL AND R21.Priority = false) -/* R22 Area */ LEFT JOIN onprc_ehr.vet_assignment R22 ON (R22.Area = d.Area AND R22.Room IS NULL AND R22.Protocol IS NULL AND R22.Project IS NULL AND R22.Priority = false) - ) placeholderAlias - diff --git a/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-20.418-20.419.sql b/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-20.418-20.419.sql new file mode 100644 index 000000000..5889279c9 --- /dev/null +++ b/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-20.418-20.419.sql @@ -0,0 +1,17 @@ +EXEC core.fn_dropifexists 'IPC_Reference_Data','onprc_ehr','TABLE'; +GO + +/****** Object: Table [onprc_ehr].[IPC_Reference_Data] Script Date: 4/27/2020 ******/ +CREATE TABLE [onprc_ehr].[IPC_Reference_Data]( + [rowId] INT IDENTITY(1,1)NOT NULL, + [value] [nvarchar](1000) NULL, + [name] [nvarchar](1000) NULL, + [remark] [nvarchar](4000) NULL, + [dateDisabled] [datetime] NULL, + [created] [datetime] NULL, + [createdBy] [int] NULL, + [modified] [datetime] NULL, + [modifiedBy] [int] NULL + + CONSTRAINT pk_IPC_Reference_Data PRIMARY KEY (rowId) + ) \ No newline at end of file diff --git a/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-23.007-23.008.sql b/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-23.007-23.008.sql new file mode 100644 index 000000000..ad07d4cfc --- /dev/null +++ b/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-23.007-23.008.sql @@ -0,0 +1,17 @@ +EXEC core.fn_dropifexists 'IPC_Reference_Data','onprc_ehr','TABLE'; +GO + +/****** Object: Table [onprc_ehr].[IPC_Reference_Data] Script Date: 4/27/2020 ******/ +CREATE TABLE [onprc_ehr].[IPC_Reference_Data]( + [rowId] INT IDENTITY(1,1)NOT NULL, + [value] [nvarchar](1000) NULL, + [name] [nvarchar](1000) NULL, + [remark] [nvarchar](4000) NULL, + [dateDisabled] [datetime] NULL, + [created] [datetime] NULL, + [createdBy] [int] NULL, + [modified] [datetime] NULL, + [modifiedBy] [int] NULL + + CONSTRAINT pk_IPC_Reference_Data PRIMARY KEY (rowId) + ) diff --git a/onprc_ehr/resources/schemas/onprc_ehr.xml b/onprc_ehr/resources/schemas/onprc_ehr.xml index 858275b36..8f9f18715 100644 --- a/onprc_ehr/resources/schemas/onprc_ehr.xml +++ b/onprc_ehr/resources/schemas/onprc_ehr.xml @@ -867,6 +867,40 @@ + + + IPC_Reference_Data + + DETAILED + + + true + + + + Value + + + + Name + + + + + End Date + + + + true + + + + true + + + +
+ diff --git a/onprc_ehr/resources/web/onprc_ehr/data/IPCClientStore.js b/onprc_ehr/resources/web/onprc_ehr/data/IPCClientStore.js new file mode 100644 index 000000000..91eda9bce --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/data/IPCClientStore.js @@ -0,0 +1,113 @@ +/* + * Copyright (c) 2013-2015 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('EHR.data.IPCClientStore', { + extend: 'EHR.data.DataEntryClientStore', + + constructor: function(){ + this.callParent(arguments); + + this.on('add', this.onAddRecord, this); + }, + + onAddRecord: function(store, records){ + Ext4.each(records, function(record){ + this.onRecordUpdate(record, ['procedureid']); + }, this); + }, + + afterEdit: function(record, modifiedFieldNames){ + this.onRecordUpdate(record, modifiedFieldNames); + + this.callParent(arguments); + }, + + onRecordUpdate: function(record, modifiedFieldNames){ + if (record.get('procedureid')){ + modifiedFieldNames = modifiedFieldNames || []; + + var lookupRec = this.getProcedureRecord(record.get('procedureid')); + if (!lookupRec) + return; + + if (lookupRec.get('remark')&& record.get('remark')== null){ + record.beginEdit(); + record.set('remark', lookupRec.get('remark')); + record.endEdit(true); + } + } + + if (modifiedFieldNames && (modifiedFieldNames.indexOf('Id') > -1 || modifiedFieldNames.indexOf('project') > -1 )){ //} modifiedFieldNames.indexOf('chargetype') > -1)){ + if (record.get('objectid')){ + var toApply = { + Id: record.get('Id'), + project: record.get('project'), + //chargetype: record.get('chargetype') + }; + + this.storeCollection.clientStores.each(function(cs){ + if (cs.storeId === this.storeCollection.collectionId + '-' + 'IPC_ServiceRequestDetails'){ + return; + } + + var projectField = cs.getFields().get('project'); + // var chargeTypeField = cs.getFields().get('chargetype'); + var hasChanges = false; + + if (cs.getFields().get('parentid')){ + if (cs.getFields().get('Id') || cs.getFields().get('project')){ + cs.each(function(r){ + if (r.get('parentid') === record.get('objectid')){ + var obj = {}; + + if (projectField){ + if (!r.get('project') || (projectField.inheritFromParent && r.get('project') !== record.get('project'))){ + obj.project = record.get('project'); + } + } + // + // if (chargeTypeField){ + // if (!r.get('chargetype') || (chargeTypeField.inheritFromParent && r.get('chargetype') !== record.get('chargetype'))){ + // obj.chargetype = record.get('chargetype'); + // } + // } + + if (r.get('Id') !== record.get('Id')){ + obj.Id = record.get('Id'); + } + + if (!Ext4.Object.isEmpty(obj)){ + r.beginEdit(); + r.set(obj); + r.endEdit(true); + hasChanges = true; + } + } + }, this); + } + } + + if (hasChanges){ + cs.fireEvent('datachanged', cs); + } + }, this); + } + } + }, + + getProcedureRecord: function(procedureId) { + var procedureStore = EHR.DataEntryUtils.getProceduresStore(); + LDK.Assert.assertNotEmpty('Unable to find procedureStore from IPCClientStore', procedureStore); + + var procRecIdx = procedureStore.findExact('rowid', procedureId); + LDK.Assert.assertTrue('Unable to find procedure record in IPCClientStore for procedureId: [' + procedureId + ']', procRecIdx > -1); + + var procedureRec = procedureStore.getAt(procRecIdx); + LDK.Assert.assertNotEmpty('Unable to find procedure record from IPCClientStore. ProcedureId was: [' + procedureId + ']', procedureRec); + + return procedureRec; + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/data/IPCStoreCollection.js b/onprc_ehr/resources/web/onprc_ehr/data/IPCStoreCollection.js new file mode 100644 index 000000000..5b387f01d --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/data/IPCStoreCollection.js @@ -0,0 +1,151 @@ +/* + * Copyright (c) 2013-2014 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('EHR.data.IPCStoreCollection', { + extend: 'EHR.data.TaskStoreCollection', + + getIPCStore: function(){ + if (this.IPCStore){ + return this.IPCStore; + } + + this.IPCStore = this.getClientStoreByName('IPC_ServiceRequestDetails'); + LDK.Assert.assertNotEmpty('Unable to find IPC store in IPCStoreCollection', this.IPCStore); + + return this.IPCStore; + }, + + getIPCRecord: function(parentid){ + if (!parentid){ + return null; + } + + var IPCStore = this.getIPCStore(); + var er; + IPCStore.each(function(r){ + if (r.get('objectid') == parentid){ + er = r; + return false; + } + }, this); + + return er; + }, + + onClientStoreUpdate: function(){ + this.doUpdateRecords(); + this.callParent(arguments); + }, + + setClientModelDefaults: function(model){ + this.callParent(arguments); + + var IPCStore = this.getIPCStore(); + if (model.store && model.store.storeId == IPCStore.storeId){ + console.log('is IPC service request, skipping'); + return; + } + + if (IPCStore.getCount() == 1){ + if (model.fields.get('parentid') && model.get('parentid') == null){ + model.data.parentid = IPCStore.getAt(0).get('objectid'); + } + } + + if (model.fields.get('parentid') && model.get('parentid')){ + //find matching IPC record and update fields if needed + var parentRec = this.getIPCRecord(model.get('parentid')); + if (parentRec){ + model.beginEdit(); + if (parentRec.get('Id') !== model.get('Id')){ + model.set('Id', parentRec.get('Id')); + } + + if (model.fields.get('date') && !model.get('date') && parentRec.get('date')){ + model.set('date', parentRec.get('date')); + } + + if (model.fields.get('project') && !model.get('project') && parentRec.get('project')){ + model.set('project', parentRec.get('project')); + } + + // if (model.fields.get('chargetype') && !model.get('chargetype') && parentRec.get('chargetype')){ + // model.set('chargetype', parentRec.get('chargetype')); + // } + + model.endEdit(true); + } + } + }, + + doUpdateRecords: function(){ + var IPCStore = this.getIPCStore(); + this.clientStores.each(function(cs){ + if (cs.storeId == IPCStore.storeId){ + return; + } + + if (cs.getFields().get('Id') == null || cs.getFields().get('parentid') == null){ + return; + } + + var isIPCChild = cs.model.prototype.sectionCfg.configSources && cs.model.prototype.sectionCfg.configSources.indexOf('IPCChild') > -1; + cs.each(function(rec){ + var IPCRec = this.getIPCRecord(rec.get('parentid')); + if (IPCRec != null){ + var obj = {}; + if (rec.get('Id') !== IPCRec.get('Id')){ + //the goal of this is to allow specific sections to avoid inheriting the Id of the parent + if (isIPCChild || !IPCRec.get('Id')) + obj.Id = IPCRec.get('Id'); + + //if the ID doesnt match, clear parentid + if (!isIPCChild){ + obj.parentid = null; + } + } + + var pf = rec.fields.get('project'); + if (pf && IPCRec.get('project')){ + if (!rec.get('project')){ + obj.project = IPCRec.get('project'); + } + else if (pf.inheritFromParent && IPCRec.get('project') !== rec.get('project')){ + obj.project = IPCRec.get('project'); + } + } + + // var cf = rec.fields.get('chargetype'); + // if (cf && IPCRec.get('chargetype')){ + // if (!rec.get('chargetype') || cf.inheritDateFromParent){ + // obj.chargetype = IPCRec.get('chargetype'); + // } + // } + + var df = rec.fields.get('date'); + if (df && IPCRec.get('date')){ + if (!rec.get('date') || df.inheritDateFromParent){ + if (!Ext4.Date.isEqual(rec.get('date'), IPCRec.get('date'))) + obj.date = IPCRec.get('date'); + } + } + + if (!Ext4.Object.isEmpty(obj)){ + rec.beginEdit(); + rec.set(obj); + rec.endEdit(true); + + // this is a slight misuse of this event. validation will queue and batch changes, rather than immediately updating each row + // individually. this is better than doing them one-by-one in large grids + if (rec.store){ + rec.store.fireEvent('validation', rec.store, rec); + } + } + } + + }, this); + }, this); + } +}); \ No newline at end of file diff --git a/onprc_ehr/resources/web/onprc_ehr/data/sources/TreatmentOrdersClientStore.js b/onprc_ehr/resources/web/onprc_ehr/data/sources/TreatmentOrdersClientStore.js deleted file mode 100644 index 67d973567..000000000 --- a/onprc_ehr/resources/web/onprc_ehr/data/sources/TreatmentOrdersClientStore.js +++ /dev/null @@ -1,91 +0,0 @@ -/* - * Copyright (c) 2013-2015 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 - */ -//Created: 7-29-2020 R.Blasa - -Ext4.define('ONPRC_EHR.data.TreatmentOrdersClientStore', { - extend: 'EHR.data.DrugAdministrationRunsClientStore', - - constructor: function(){ - this.callParent(arguments); - - this.on('add', this.onAddRecord, this); - }, - - onAddRecord: function(store, records){ - Ext4.each(records, function(record){ - this.onRecordUpdate(record, ['objectid', 'code']); - }, this); - }, - - afterEdit: function(record, modifiedFieldNames){ - this.onRecordUpdate(record, modifiedFieldNames); - - this.callParent(arguments); - }, - - onRecordUpdate: function(record, modifiedFieldNames){ - if (record.get('code')){ - modifiedFieldNames = modifiedFieldNames || []; - - if (modifiedFieldNames.indexOf('code') == -1){ - return; - } - - /* Changed by Kollil on 10/11/2023, - Requested by Cassie to remove the verbiage in the remark field for the MPA medication. Refer to tkt # 9939 - The default setting for this medication in DB schema browser is updated too. - */ - if (record.get('code') == 'E-85760'){ - record.beginEdit(); - record.set('remark', ''); - record.endEdit(true); - } - // if (record.get('code') == 'E-85760' && record.get('remark') == null){ - // record.beginEdit(); - // record.set('remark', 'Please make a clinical prime entry at each administration once the administration is complete.'); - // record.endEdit(true); - // } - - if (!this.formularyStore){ - LDK.Utils.logToServer({ - message: 'Unable to find formulary store in DrugAdministrationRunsClientStore' - }); - console.error('Unable to find formulary store in DrugAdministrationRunsClientStore'); - - return; - } - - var values = this.formularyStore.getFormularyValues(record.get('code')); - if (!Ext4.Object.isEmpty(values)){ - var params = {}; - - for (var fieldName in this.fieldMap){ - if (!this.getFields().get(fieldName)){ - continue; - } - - if (modifiedFieldNames.indexOf(this.fieldMap[fieldName]) != -1){ - //console.log('field already set: ' + fieldName); - continue; - } - - var def = values[fieldName]; - if (Ext4.isDefined(def)){ - params[this.fieldMap[fieldName]] = def; - } - } - - if (!LABKEY.Utils.isEmptyObj(params)){ - record.beginEdit(); - record.set(params); - record.endEdit(true); - } - } - } - } - - -}); diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_CassettePrinting.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_CassettePrinting.js new file mode 100644 index 000000000..2afe146a5 --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_CassettePrinting.js @@ -0,0 +1,58 @@ +/** + * User: Kolli + * Date: 4/10/2020 + * Time: 10:36 AM + */ +EHR.model.DataModelManager.registerMetadata('CassettePrinting', { + allQueries: { + }, + + byQuery: { + 'study.IPC_CassettePrinting': { + + tissueType: { + columnConfig: { + width: 250 + } + }, + + PILabel: { + header:"Additional text on cassette", + columnConfig: { + width: 200 + } + }, + + cassetteColor: { + header:"Cassette Color", + columnConfig: { + width: 200 + } + }, + + remark: { + header:"Remark", + hidden: false, + columnConfig: { + width: 250 + } + }, + + performedBy: { + defaultValue: LABKEY.Security.currentUser.displayName, + columnConfig: { + width: 150 + } + } + // , + // + // qcstate: { + // hidden: true, + // defaultValue: 21 + // } + + } + + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Child.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Child.js new file mode 100644 index 000000000..b481aa490 --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Child.js @@ -0,0 +1,21 @@ +/* + * Copyright (c) 2013-2014 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('IPC_Child', { + allQueries: { + Id: { + editable: false, + columnConfig: { + editable: false + } + }, + date: { + inheritDateFromParent: true + } + + } + + +}); \ No newline at end of file diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Other.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Other.js new file mode 100644 index 000000000..6fee8a8b6 --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Other.js @@ -0,0 +1,39 @@ +/** + * User: Kolli + * Date: 4/10/2020 + * Time: 10:36 AM + */ + +EHR.model.DataModelManager.registerMetadata('IPC_Other', { + allQueries: { + }, + + byQuery: { + 'study.IPC_Other': { + + tissueType: { + columnConfig: { + width: 250 + } + }, + + serviceAndProducts: { + header:"Service & Products", + hidden: false, + columnConfig: { + width: 250 + } + }, + + performedBy: { + defaultValue: LABKEY.Security.currentUser.displayName, + columnConfig: { + width: 150 + } + } + + } + + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_ProcessingEmbedding.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_ProcessingEmbedding.js new file mode 100644 index 000000000..3c00ead12 --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_ProcessingEmbedding.js @@ -0,0 +1,71 @@ +/** + * User: Kolli + * Date: 4/10/2020 + * Time: 10:36 AM + */ +EHR.model.DataModelManager.registerMetadata('ProcessingEmbedding', { + allQueries: { + }, + byQuery: { + 'study.IPC_ProcessingEmbedding': { + + tissueType: { + columnConfig: { + width: 250 + } + }, + + embedding: { + columnConfig: { + width: 200 + } + }, + + fixationMethod: { + header:"Initial Fixative", + columnConfig: { + width: 200 + } + }, + + fixationDuration: { + header:"Fixation Duration", + columnConfig: { + width: 150 + } + }, + + currentFixative: { + header:"Current Fixative", + columnConfig: { + width: 150 + } + }, + + processingType: { + header:"Processing Type", + columnConfig: { + width: 250 + } + }, + + embeddingIns: { + header:"Embedding Instructions", + hidden: false, + columnConfig: { + width: 250 + } + }, + + performedBy: { + defaultValue: LABKEY.Security.currentUser.displayName, + columnConfig: { + width: 150 + } + } + + } + + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Sectioning.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Sectioning.js new file mode 100644 index 000000000..983f0a496 --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Sectioning.js @@ -0,0 +1,58 @@ +/** + * User: Kolli + * Date: 4/10/2020 + * Time: 10:36 AM + */ +EHR.model.DataModelManager.registerMetadata('Sectioning', { + allQueries: { + }, + byQuery: { + 'study.IPC_Sectioning': { + + tissueType: { + columnConfig: { + width: 250 + } + }, + + paraffinSectioning: { + header:"Paraffin Sectioning", + columnConfig: { + width: 200 + } + }, + + sectionThickness: { + header:"Paraffin Section Thickness", + columnConfig: { + width: 200 + } + }, + + frozenSectioning: { + header:"Frozen Section Thickness", + columnConfig: { + width: 200 + } + }, + + specialIns: { + header:"Special Instructions", + hidden: false, + columnConfig: { + width: 250 + } + }, + + performedBy: { + defaultValue: LABKEY.Security.currentUser.displayName, + columnConfig: { + width: 150 + } + } + + } + + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_ServiceRequestDetails.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_ServiceRequestDetails.js new file mode 100644 index 000000000..6e8c1b2fa --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_ServiceRequestDetails.js @@ -0,0 +1,102 @@ +/** + * User: Kolli + * Date: 4/10/2020 + * Time: 10:36 AM + */ +EHR.model.DataModelManager.registerMetadata('ServiceRequestDetails', { + allQueries: { + }, + byQuery: { + 'study.IPC_ServiceRequestDetails': { + + project: { + header:"Center Project", + columnConfig: { + width: 150 + } + }, + + requestedBy: { + header:"Requested By", + columnConfig: { + width: 150 + } + }, + + email: { + header:"Email", + columnConfig: { + width: 150 + } + }, + + department: { + header:"Department", + columnConfig: { + width: 150 + } + }, + + pathologist: { + xtype: 'combo', + header:'Pathologist', + hidden: false, + lookup: {schemaName: 'study', queryName: 'IPC_Pathologist', displayColumn:'name' }, + + editorConfig: { + listConfig: { + //innerTpl: '{[values.lastName + (values.firstName ? ", " + values.firstName : "")]}', + innerTpl: '{[(values.name)]}', + getInnerTpl: function(){ + return this.innerTpl; + } + } + }, + columnConfig: { + width: 200 + } + }, + + investigator: { + xtype: 'combo', + header: 'Investigator', + hidden: false, + lookup: {schemaName: 'study', queryName: 'IPC_Investigators', displayColumn: 'name'}, + editorConfig: { + listConfig: { + // innerTpl: '{[values.lastName + (values.firstName ? ", " + values.firstName : "")]}', + innerTpl: '{[(values.name)]}', + getInnerTpl: function(){ + return this.innerTpl; + } + } + }, + columnConfig: { + width: 200 + } + }, + + sampleLocation: { + xtype: 'combo', + header: 'Sample DropOff/PickUp Location', + hidden: true, + lookup: {schemaName: 'study', queryName: 'IPC_Locations', displayColumn: 'room'}, + + editorConfig: { + listConfig: { + innerTpl: '{[(values.room)]}', + getInnerTpl: function(){ + return this.innerTpl; + } + } + }, + columnConfig: { + width: 200 + } + } + + } + + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_SlidePrinting.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_SlidePrinting.js new file mode 100644 index 000000000..fdac82072 --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_SlidePrinting.js @@ -0,0 +1,45 @@ +/** + * User: Kolli + * Date: 4/10/2020 + * Time: 10:36 AM + */ +EHR.model.DataModelManager.registerMetadata('SlidePrinting', { + allQueries: { + }, + byQuery: { + 'study.IPC_SlidePrinting': { + + tissueType: { + columnConfig: { + width: 250 + } + }, + + projectNotes: { + header:"Project Notes", + hidden: false, + columnConfig: { + width: 250 + } + }, + + additionalText: { + header:"Additional text on slide", + hidden: false, + columnConfig: { + width: 250 + } + }, + + performedBy: { + defaultValue: LABKEY.Security.currentUser.displayName, + columnConfig: { + width: 150 + } + } + + } + + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Staining.js b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Staining.js new file mode 100644 index 000000000..78c5f0d8b --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/model/sources/IPC_Staining.js @@ -0,0 +1,83 @@ +/** + * User: Kolli + * Date: 4/10/2020 + * Time: 10:36 AM + */ +EHR.model.DataModelManager.registerMetadata('Staining', { + allQueries: { + }, + + byQuery: { + 'study.IPC_Staining': { + + tissueType: { + columnConfig: { + width: 250 + } + }, + + HAndE: { + header:"H&E", + columnConfig: { + width: 150 + } + }, + + specialStain: { + header:"Special Stain", + columnConfig: { + width: 150 + } + }, + + IHC: { + header:"IHC", + columnConfig: { + width: 150 + } + }, + + IHCPrimaryAntibody: { + header:"IHC Primary Antibody", + hidden: false, + columnConfig: { + width: 200 + } + }, + + irrelevantAntibody: { + header:"Irrelevant Antibody", + hidden: false, + columnConfig: { + width: 200 + } + }, + + RNAScope: { + header:"RNA Scope", + hidden: false, + columnConfig: { + width: 150 + } + }, + + other: { + header:"Other", + hidden: false, + columnConfig: { + width: 150 + } + }, + + performedBy: { + defaultValue: LABKEY.Security.currentUser.displayName, + columnConfig: { + width: 150 + } + } + + } + + } + +}); diff --git a/onprc_ehr/resources/web/onprc_ehr/window/IPC_CopyFromSectionWindow.js b/onprc_ehr/resources/web/onprc_ehr/window/IPC_CopyFromSectionWindow.js new file mode 100644 index 000000000..889a8cbcb --- /dev/null +++ b/onprc_ehr/resources/web/onprc_ehr/window/IPC_CopyFromSectionWindow.js @@ -0,0 +1,398 @@ +/* + * Copyright (c) 2013-2017 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +/** + * @cfg targetGrid + * @cfg parentStore + * @cfg sourceLabel + * Created: Kollil, 5/19/2020 + */ +Ext4.define('ONPRC_EHR.window.IPC_CopyFromSectionWindow', { + extend: 'Ext.window.Window', + + initComponent: function(){ + this.getParentRecords(); + + Ext4.applyIf(this, { + modal: true, + width: 1000, + closeAction: 'destroy', + title: 'Copy From ' + this.sourceLabel, + bodyStyle: 'padding: 5px;', + defaults: { + border: false + }, + items: [{ + html: 'This helper allows you to populate 1 row for each animal from the ' + this.sourceLabel + ' section. Choose which IDs to add from the list below.', + style: 'margin-bottom: 10px;' + },{ + xtype: 'checkbox', + fieldLabel: 'Bulk Edit Values', + labelWidth: 150, + helpPopup: 'If checked, you will be prompted with a screen that lets you bulk edit the records that will be created. This is often very useful when adding many similar records.', + itemId: 'chooseValues', + style: 'margin-bottom: 10px;' + },{ + itemId: 'animalIds', + items: this.getInitialItems() + }], + buttons: [{ + text: 'Submit', + itemId: 'submitBtn', + scope: this, + handler: this.onSubmit + },{ + text: 'Close', + handler: function(btn){ + btn.up('window').close(); + } + }] + }); + + this.callParent(); + + this.on('beforeshow', function(window){ + if (!this.parentRecords.length){ + Ext4.Msg.alert('No Records', 'There are no records to copy. Note: only records with an Id/Date can be copied.'); + return false; + } + }, this); + }, + + getParentRecords: function(){ + var records = []; + this.parentStore.each(function(r){ + if (r.get('Id') && r.get('date')){ + records.push(r); + } + }, this); + + this.parentRecords = records; + + return records; + }, + + getExistingIds: function(keyFields){ + var map = {}; + this.targetGrid.store.each(function(r){ + var key = this.getKeyValue(r, keyFields); + if (r.get('Id')) + map[key] = true; + }, this); + + return map; + }, + + getKeyValue: function(record, keyFields){ + var key = []; + Ext4.Array.forEach(keyFields, function(kf){ + if (record.get(kf)) + key.push(record.get(kf)); + }, this); + + return key.join ('||'); + }, + + getInitialItems: function(){ + var items = [{ + html: 'Animal' + },{ + html: 'Date' + },{ + html: 'Project' + }] + + if (this.targetGrid.store.getFields().get('chargetype')) + { + items.push({ + html: 'Charge Unit' + }); + } + + if (this.targetGrid.store.getFields().get('tissueType')) + { + items.push({ + html: 'Tissue Type' + }); + } + + items = items.concat([{ + html: 'Performed By' + },{ + html: 'Skip?' + }]); + + var keys = {}, key; + var keyFields = ['Id', 'date', 'tissueType']; +// if (this.targetGrid.store.getFields().get('parentid')){ +// keyFields.push('parentid'); +// } +// if (this.targetGrid.store.getFields().get('runid')){ +// keyFields.push('runid'); +// } + + //console.log(keyFields); + var orderedKeys = []; + Ext4.Array.forEach(this.parentRecords, function(record){ + key = this.getKeyValue(record, keyFields); + if (orderedKeys.indexOf(key) == -1){ + orderedKeys.push(key); + } + + keys[key] = keys[key] || { + Id: record.get('Id'), +// parentid: keyFields.indexOf('parentid') > -1 ? record.get('parentid') : null, +// runid: keyFields.indexOf('runid') > -1 ? record.get('runid') : null, + performedby: [], + projects: [], + chargeUnits: [], + tissueTypes: [], + dates: [], + total: 0 + }; + + keys[key].total++; + if (record.get('performedby')) + keys[key].performedby.push(record.get('performedby')); + if (record.get('project')) + keys[key].projects.push(record.get('project')); + if (record.fields.get('chargetype') && record.get('chargetype')) + keys[key].chargeUnits.push(record.get('chargetype')); + + if (record.fields.get('tissueType') && record.get('tissueType')) + keys[key].tissueTypes.push(record.get('tissueType')); + + keys[key].dates.push(record.get('date')) + }, this); + + var existingIds = this.getExistingIds(keyFields); + Ext4.Array.forEach(orderedKeys, function(key){ + var o = keys[key]; + + items.push({ + xtype: 'displayfield', + key: key, + value: o.Id, + fieldName: 'Id' + }); + + var dates = []; + var minDate; + Ext4.Array.forEach(o.dates, function(date){ + if (!minDate || date < minDate) + minDate = date; + + dates.push(date.format(LABKEY.extDefaultDateTimeFormat)); + }, this); + + o.performedby = Ext4.unique(o.performedby); + var performedby = o.performedby.length == 1 ? o.performedby[0] : null; + + o.projects = Ext4.unique(o.projects); + var project = o.projects.length == 1 ? o.projects[0] : null; + + o.chargeUnits = Ext4.unique(o.chargeUnits); + var chargeUnit = o.chargeUnits.length == 1 ? o.chargeUnits[0] : null; + + o.tissueTypes = Ext4.unique(o.tissueTypes); + var tissueType = o.tissueTypes.length == 1 ? o.tissueTypes[0] : null; + + + items.push({ + xtype: 'xdatetime', + width: 300, + format: LABKEY.extDefaultDateTimeFormat, + timeFormat: 'H:i', + fieldName: 'date', + key: key, + value: minDate + }); + + items.push({ + xtype: 'ehr-projectfield', + matchFieldWidth: false, + showInactive: true, + fieldLabel: null, + width: 100, + fieldName: 'project', + key: key, + value: project + }); + + if (this.targetGrid.store.getFields().get('chargetype')){ + var cfg = LABKEY.ext4.Util.getDefaultEditorConfig(this.targetGrid.store.getFields().get('chargetype')); + + items.push(Ext4.apply(cfg, { + matchFieldWidth: false, + showInactive: true, + fieldLabel: null, + width: 160, + fieldName: 'chargetype', + key: key, + value: chargeUnit + })); + } + + if (this.targetGrid.store.getFields().get('tissueType')){ + var cfg = LABKEY.ext4.Util.getDefaultEditorConfig(this.targetGrid.store.getFields().get('tissueType')); + + items.push(Ext4.apply(cfg, { + matchFieldWidth: false, + showInactive: true, + fieldLabel: null, + width: 160, + fieldName: 'tissueType', + key: key, + value: tissueType + })); + } + + items.push({ + xtype: 'textfield', + width: 200, + fieldName: 'performedby', + key: key, + value: performedby + }); + + items.push({ + xtype: 'checkbox', + key: key, + fieldName: 'exclude', + checked: existingIds[key] + }); + }, this); + + return [{ + itemId: 'theTable', + border: false, + layout: { + type: 'table', + //columns: this.targetGrid.store.getFields().get('chargetype') ? 6 : 5, + columns: this.targetGrid.store.getFields().get('tissueType') ? 6 : 5 + }, + defaults: { + border: false, + style: 'margin: 5px;' + }, + items: items + }] + }, + + getRows: function(){ + var table = this.down('#theTable'); + var orderedKeys = []; + var rowMap = {}; + table.items.each(function(item){ + if (item.fieldName){ + if (orderedKeys.indexOf(item.key) == -1) + orderedKeys.push(item.key); + + rowMap[item.key] = rowMap[item.key] || {}; + rowMap[item.key][item.fieldName] = item.getValue ? item.getValue() : item.value; + } + }, this); + + var ret = []; + Ext4.Array.forEach(orderedKeys, function(key){ + ret.push(rowMap[key]); + }, this); + + return ret; + }, + + onSubmit: function(btn){ + var toAdd = []; + Ext4.Array.forEach(this.getRows(), function(data){ + if (!data.exclude){ + toAdd.push(this.targetGrid.store.createModel(data)); + } + }, this); + + if (toAdd.length){ + var choose = this.down('#chooseValues').getValue(); + if (choose){ + Ext4.create('EHR.window.BulkEditWindow', { + suppressConfirmMsg: true, + records: toAdd, + targetStore: this.targetGrid.store, + formConfig: this.targetGrid.formConfig + }).show(); + this.close(); + } + else { + this.targetGrid.store.add(toAdd); + } + } + + this.close(); + } +}); + + +EHR.DataEntryUtils.registerGridButton('IPC_COPYFROMSECTION', function(config){ + return Ext4.Object.merge({ + text: 'IPC Copy From Section', + xtype: 'button', + tooltip: 'Click to copy records from one of the other sections', + listeners: { + beforerender: function(btn){ + var grid = btn.up('gridpanel'); + LDK.Assert.assertNotEmpty('Unable to find gridpanel in COPYFROMSECTION button', grid); + + btn.grid = grid; + + btn.appendButtons.call(btn); + } + }, + menu: { + xtype: 'menu', + items: [{ + text: 'Loading...' + }] + }, + appendButtons: function(){ + this.dataEntryPanel = this.grid.up('ehr-dataentrypanel'); + LDK.Assert.assertNotEmpty('Unable to find dataEntryPanel in COPYFROMSECTION button', this.dataEntryPanel); + + var toAdd = []; + Ext4.Array.forEach(this.dataEntryPanel.formConfig.sections, function(section){ + if (section.name == this.grid.formConfig.name){ + return; + } + + var store = this.dataEntryPanel.storeCollection.getClientStoreByName(section.name); + if (store){ + //only allow copying from sections with an ID field + if (!store.getFields().get('Id')){ + return; + } + + toAdd.push({ + text: section.label, + scope: this, + handler: function(menu){ + Ext4.create('ONPRC_EHR.window.IPC_CopyFromSectionWindow', { + targetGrid: this.grid, + sourceLabel: section.label, + parentStore: store + }).show(); + } + }); + } + }, this); + + this.menu.removeAll(); + if (toAdd.length){ + this.menu.add(toAdd); + } + else { + this.menu.add({ + text: 'There are no other sections' + }) + } + } + }); +}); \ No newline at end of file diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java b/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java index edbb6bde0..0c12e543c 100644 --- a/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java +++ b/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java @@ -123,7 +123,7 @@ public String getName() @Override public @Nullable Double getSchemaVersion() { - return 23.007; + return 23.008; } @Override @@ -550,13 +550,11 @@ public String toString() //Added: 7/10/2019 by Kolli EHRService.get().registerFormType(new DefaultDataEntryFormFactory(PMICDataEntryFormType.class, this)); - //Added: 1/13/2021 Kolli -// EHRService.get().registerFormType(new DefaultDataEntryFormFactory(ARTCoreRequestFormType.class, this)); - - //Added: 8/10/2019 Kolli -// EHRService.get().registerFormType(new DefaultDataEntryFormFactory(IPCRequestFormType.class, this)); + //Created: 8/10/2019 Kolli + //Modified: 10/20/2023 Kolli + EHRService.get().registerFormType(new DefaultDataEntryFormFactory(IPCRequestFormType.class, this)); -// Added: 11-21-2017 R.Blasa + //Added: 11-21-2017 R.Blasa EHRService.get().registerFormType(new DefaultDataEntryFormFactory(ProcedureRequestBulkEditFormType.class, this)); EHRService.get().registerFormType(new DefaultDataEntryFormFactory(RecordAmendmentFormType.class, this)); @@ -576,8 +574,6 @@ public String toString() //Added: 6-6-2022 R.Blasa EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NecropsyRequestForm.class, this)); - - //single section forms EHRService.get().registerSingleFormOverride(new SingleQueryFormProvider(this, "study", "treatment_order", new MedicationsQueryFormSection("study", "Treatment Orders", "Medication/Treatment Orders"))); EHRService.get().registerSingleFormOverride(new SingleQueryFormProvider(this, "study", "drug", new MedicationsQueryFormSection("study", "Drug Administration", "Medication/Treatments Given"))); diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPCRequestFormType.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPCRequestFormType.java new file mode 100644 index 000000000..2b3767048 --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPCRequestFormType.java @@ -0,0 +1,40 @@ +package org.labkey.onprc_ehr.dataentry; + +import org.labkey.api.ehr.dataentry.DataEntryFormContext; +import org.labkey.api.ehr.dataentry.TaskForm; +import org.labkey.api.ehr.dataentry.TaskFormSection; +import org.labkey.api.module.Module; +import org.labkey.api.view.template.ClientDependency; + +import java.util.Arrays; + +/** + * User: Kolli + * Date: 7/7/19 + * Time: 10:36 AM + */ +public class IPCRequestFormType extends TaskForm +{ + public static final String NAME = "IPC SERVICE REQUEST"; + + public IPCRequestFormType(DataEntryFormContext ctx, Module owner) + { + super(ctx, owner, NAME, "Histology Service Request", "Imaging", Arrays.asList( + new TaskFormSection(), + new IPC_ServiceRequestDetailsFormSection("Service Request Details"), + new AnimalDetailssFormSection(), + new IPC_CassettePrintingFormSection(), + new IPC_ProcessingEmbeddingFormSection(), + new IPC_SectioningFormSection(), + new IPC_StainingFormSection(), + new IPC_SlidePrintingFormSection(), + new IPC_OtherFormSection() + )); + + setStoreCollectionClass("EHR.data.IPCStoreCollection"); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/data/IPCStoreCollection.js")); + } + +} + + diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_CassettePrintingFormSection.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_CassettePrintingFormSection.java new file mode 100644 index 000000000..fc08a4d65 --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_CassettePrintingFormSection.java @@ -0,0 +1,50 @@ +package org.labkey.onprc_ehr.dataentry; + +import org.labkey.api.ehr.EHRService; +import org.labkey.api.ehr.dataentry.SimpleGridPanel; +import org.labkey.api.view.template.ClientDependency; +import java.util.List; + + +/** + * User: Kollil + * Date: 4/01/2020 + * Time: 10:36 AM + */ +public class IPC_CassettePrintingFormSection extends SimpleGridPanel +{ + public IPC_CassettePrintingFormSection() + { + this(EHRService.FORM_SECTION_LOCATION.Body); + } + + public IPC_CassettePrintingFormSection(EHRService.FORM_SECTION_LOCATION location) + { + super("study", "IPC_CassettePrinting", "Cassette Printing", location); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_CassettePrinting.js")); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Child.js")); + addConfigSource("IPC_Child"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/window/IPC_CopyFromSectionWindow.js")); + + addConfigSource("CassettePrinting"); + } + + @Override + public List getTbarButtons() + { + List defaultButtons = super.getTbarButtons(); + + if (defaultButtons.contains("COPYFROMSECTION")) + { + int idx = defaultButtons.indexOf("COPYFROMSECTION"); + defaultButtons.remove("COPYFROMSECTION"); + defaultButtons.add(idx, "IPC_COPYFROMSECTION"); + } + + return defaultButtons; + } + +} + diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_OtherFormSection.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_OtherFormSection.java new file mode 100644 index 000000000..597ddcebf --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_OtherFormSection.java @@ -0,0 +1,44 @@ +package org.labkey.onprc_ehr.dataentry; + +import org.labkey.api.ehr.EHRService; +import org.labkey.api.ehr.dataentry.SimpleGridPanel; +import org.labkey.api.view.template.ClientDependency; +import java.util.List; + +/** + * User: Kolli + * Date: 4/01/2020 + * Time: 10:36 AM + */ +public class IPC_OtherFormSection extends SimpleGridPanel +{ + public IPC_OtherFormSection() + { + this(EHRService.FORM_SECTION_LOCATION.Body); + } + + public IPC_OtherFormSection(EHRService.FORM_SECTION_LOCATION location) + { + super("study", "IPC_Other", "Other", location); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Other.js")); + addConfigSource("IPC_Other"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/window/IPC_CopyFromSectionWindow.js")); + } + + @Override + public List getTbarButtons() + { + List defaultButtons = super.getTbarButtons(); + + if (defaultButtons.contains("COPYFROMSECTION")) + { + int idx = defaultButtons.indexOf("COPYFROMSECTION"); + defaultButtons.remove("COPYFROMSECTION"); + defaultButtons.add(idx, "IPC_COPYFROMSECTION"); + } + + return defaultButtons; + } + +} \ No newline at end of file diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_ProcessingEmbeddingFormSection.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_ProcessingEmbeddingFormSection.java new file mode 100644 index 000000000..dd147b6f6 --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_ProcessingEmbeddingFormSection.java @@ -0,0 +1,48 @@ +package org.labkey.onprc_ehr.dataentry; + +import org.labkey.api.ehr.EHRService; +import org.labkey.api.ehr.dataentry.SimpleGridPanel; +import org.labkey.api.view.template.ClientDependency; +import java.util.List; + +/** + * User: Kolli + * Date: 4/01/2020 + * Time: 10:36 AM + */ +public class IPC_ProcessingEmbeddingFormSection extends SimpleGridPanel +{ + public IPC_ProcessingEmbeddingFormSection() + { + this(EHRService.FORM_SECTION_LOCATION.Body); + } + + public IPC_ProcessingEmbeddingFormSection(EHRService.FORM_SECTION_LOCATION location) + { + super("study", "IPC_ProcessingEmbedding", "Tissue Processing / Embedding", location); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_ProcessingEmbedding.js")); + + addConfigSource("ProcessingEmbedding"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Child.js")); + addConfigSource("IPC_Child"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/window/IPC_CopyFromSectionWindow.js")); + } + + @Override + public List getTbarButtons() + { + List defaultButtons = super.getTbarButtons(); + + if (defaultButtons.contains("COPYFROMSECTION")) + { + int idx = defaultButtons.indexOf("COPYFROMSECTION"); + defaultButtons.remove("COPYFROMSECTION"); + defaultButtons.add(idx, "IPC_COPYFROMSECTION"); + } + + return defaultButtons; + } + +} \ No newline at end of file diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_SectioningFormSection.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_SectioningFormSection.java new file mode 100644 index 000000000..9e1bd4cdd --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_SectioningFormSection.java @@ -0,0 +1,47 @@ +package org.labkey.onprc_ehr.dataentry; + +import org.labkey.api.ehr.EHRService; +import org.labkey.api.ehr.dataentry.SimpleGridPanel; +import org.labkey.api.view.template.ClientDependency; +import java.util.List; + +/** + * User: Kolli + * Date: 4/01/2020 + * Time: 10:36 AM + */ +public class IPC_SectioningFormSection extends SimpleGridPanel +{ + public IPC_SectioningFormSection() + { + this(EHRService.FORM_SECTION_LOCATION.Body); + } + + public IPC_SectioningFormSection(EHRService.FORM_SECTION_LOCATION location) + { + super("study", "IPC_Sectioning", "Sectioning", location); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Sectioning.js")); + addConfigSource("Sectioning"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Child.js")); + addConfigSource("IPC_Child"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/window/IPC_CopyFromSectionWindow.js")); + } + + @Override + public List getTbarButtons() + { + List defaultButtons = super.getTbarButtons(); + + if (defaultButtons.contains("COPYFROMSECTION")) + { + int idx = defaultButtons.indexOf("COPYFROMSECTION"); + defaultButtons.remove("COPYFROMSECTION"); + defaultButtons.add(idx, "IPC_COPYFROMSECTION"); + } + + return defaultButtons; + } + +} \ No newline at end of file diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_ServiceRequestDetailsFormSection.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_ServiceRequestDetailsFormSection.java new file mode 100644 index 000000000..c623a20bf --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_ServiceRequestDetailsFormSection.java @@ -0,0 +1,22 @@ +/* +// * User: Kolli +// * Date: 4/01/2020 +// * Time: 10:36 AM + */ + +package org.labkey.onprc_ehr.dataentry; + +import org.labkey.api.ehr.dataentry.SimpleFormPanelSection; +import org.labkey.api.view.template.ClientDependency; + +public class IPC_ServiceRequestDetailsFormSection extends SimpleFormPanelSection +{ + public IPC_ServiceRequestDetailsFormSection(String label) + { + super("study", "IPC_ServiceRequestDetails", label); + setTemplateMode(TEMPLATE_MODE.NONE); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_ServiceRequestDetails.js")); + addConfigSource("ServiceRequestDetails"); + } +} + diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_SlidePrintingFormSection.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_SlidePrintingFormSection.java new file mode 100644 index 000000000..e07b9d149 --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_SlidePrintingFormSection.java @@ -0,0 +1,46 @@ +package org.labkey.onprc_ehr.dataentry; + +import org.labkey.api.ehr.EHRService; +import org.labkey.api.ehr.dataentry.SimpleGridPanel; +import org.labkey.api.view.template.ClientDependency; +import java.util.List; + +/** + * User: Kolli + * Date: 4/01/2020 + * Time: 10:36 AM + */ +public class IPC_SlidePrintingFormSection extends SimpleGridPanel +{ + public IPC_SlidePrintingFormSection() + { + this(EHRService.FORM_SECTION_LOCATION.Body); + } + + public IPC_SlidePrintingFormSection(EHRService.FORM_SECTION_LOCATION location) + { + super("study", "IPC_SlidePrinting", "Slide Printing (No Sectioning)", location); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_SlidePrinting.js")); + addConfigSource("SlidePrinting"); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Child.js")); + addConfigSource("IPC_Child"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/window/IPC_CopyFromSectionWindow.js")); + } + + @Override + public List getTbarButtons() + { + List defaultButtons = super.getTbarButtons(); + + if (defaultButtons.contains("COPYFROMSECTION")) + { + int idx = defaultButtons.indexOf("COPYFROMSECTION"); + defaultButtons.remove("COPYFROMSECTION"); + defaultButtons.add(idx, "IPC_COPYFROMSECTION"); + } + + return defaultButtons; + } + +} \ No newline at end of file diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_StainingFormSection.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_StainingFormSection.java new file mode 100644 index 000000000..28120b2ea --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/IPC_StainingFormSection.java @@ -0,0 +1,45 @@ +package org.labkey.onprc_ehr.dataentry; +import org.labkey.api.ehr.EHRService; +import org.labkey.api.ehr.dataentry.SimpleGridPanel; +import org.labkey.api.view.template.ClientDependency; +import java.util.List; + +/** + * User: Kolli + * Date: 4/01/2020 + * Time: 10:36 AM + */ +public class IPC_StainingFormSection extends SimpleGridPanel +{ + public IPC_StainingFormSection() + { + this(EHRService.FORM_SECTION_LOCATION.Body); + } + + public IPC_StainingFormSection(EHRService.FORM_SECTION_LOCATION location) + { + super("study", "IPC_Staining", "Staining", location); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Staining.js")); + addConfigSource("Staining"); + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/model/sources/IPC_Child.js")); + addConfigSource("IPC_Child"); + + addClientDependency(ClientDependency.supplierFromPath("onprc_ehr/window/IPC_CopyFromSectionWindow.js")); + } + + @Override + public List getTbarButtons() + { + List defaultButtons = super.getTbarButtons(); + + if (defaultButtons.contains("COPYFROMSECTION")) + { + int idx = defaultButtons.indexOf("COPYFROMSECTION"); + defaultButtons.remove("COPYFROMSECTION"); + defaultButtons.add(idx, "IPC_COPYFROMSECTION"); + } + + return defaultButtons; + } + +} \ No newline at end of file diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/MedSignoffFormType.java b/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/MedSignoffFormType.java deleted file mode 100644 index a9c8fbfef..000000000 --- a/onprc_ehr/src/org/labkey/onprc_ehr/dataentry/MedSignoffFormType.java +++ /dev/null @@ -1,86 +0,0 @@ -/* - * Copyright (c) 2013-2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.onprc_ehr.dataentry; - -import org.labkey.api.ehr.EHRService; -import org.labkey.api.ehr.dataentry.AnimalDetailsFormSection; -import org.labkey.api.ehr.dataentry.DataEntryFormContext; -import org.labkey.api.ehr.dataentry.NonStoreFormSection; -import org.labkey.api.ehr.dataentry.TaskForm; -import org.labkey.api.ehr.dataentry.TaskFormSection; -import org.labkey.api.ehr.dataentry.DrugAdministrationFormSection; -import org.labkey.api.ehr.security.EHRClinicalEntryPermission; -import org.labkey.api.module.Module; -import org.labkey.api.module.ModuleLoader; -import org.labkey.api.security.Group; -import org.labkey.api.security.GroupManager; -import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.view.template.ClientDependency; -import org.labkey.security.xml.GroupEnumType; - -import java.util.Arrays; - -/** - * User: bimber - * Date: 7/29/13 - * Time: 5:03 PM - */ -public class MedSignoffFormType extends TaskForm -{ - public static final String NAME = "medsignoff"; - public static final String LABEL = "Post-administration Med Verification"; //Changed by Kollil on 10/11/23, Refer to tkt #9939 - - public MedSignoffFormType(DataEntryFormContext ctx, Module owner) - { - super(ctx, owner, NAME, LABEL, "Clinical", Arrays.asList( - new TaskFormSection(), - //Added 2-19-2016 Blasa - new NonStoreFormSection("Treatment Template Helper", "Treatment Template Helper", "onprc_AddScheduledTreatmentPanel", Arrays.asList(ClientDependency.supplierFromPath("/onprc_ehr/panel/AddScheduledTreatmentPanel.js"))), - - new AnimalDetailsFormSection(), - new DrugAdministrationFormSection(ClientDependency.supplierFromPath("onprc_ehr/window/ONPRC_AddScheduledTreatmentWindow.js")) - /* new TreatmentOrdersFormSection()*/ - )); - - if (ctx.getContainer().getActiveModules().contains(ModuleLoader.getInstance().getModule("onprc_billing"))) - { - addSection(new MiscChargesFormSection(EHRService.FORM_SECTION_LOCATION.Body)); - } - - } - - @Override - protected boolean canInsert() - { - if (!getCtx().getContainer().hasPermission(getCtx().getUser(), EHRClinicalEntryPermission.class)) - return false; - - return super.canInsert(); - } - - //Modified: 12-5-2019 R.Blasa - @Override - public boolean isVisible() - { - Group g = GroupManager.getGroup(getCtx().getContainer(), "ASB Support", GroupEnumType.SITE); - if (g != null && getCtx().getUser().isInGroup(g.getUserId()) && !getCtx().getContainer().hasPermission(getCtx().getUser(), AdminPermission.class)) - { - return false; - } - - return super.isVisible(); - } -} diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/notification/BehaviorNotification.java b/onprc_ehr/src/org/labkey/onprc_ehr/notification/BehaviorNotification.java deleted file mode 100644 index fe06dda55..000000000 --- a/onprc_ehr/src/org/labkey/onprc_ehr/notification/BehaviorNotification.java +++ /dev/null @@ -1,385 +0,0 @@ -/* - * Copyright (c) 2013-2016 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.onprc_ehr.notification; - -import org.apache.commons.lang3.time.DateUtils; -import org.json.JSONObject; -import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; -import org.labkey.api.module.Module; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryDefinition; -import org.labkey.api.query.QueryException; -import org.labkey.api.query.QueryService; -import org.labkey.api.query.UserSchema; -import org.labkey.api.security.User; -import org.labkey.api.util.PageFlowUtil; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Calendar; -import java.util.Collection; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -/** - * User: bimber - * Date: 4/5/13 - * Time: 2:25 PM - */ -public class BehaviorNotification extends ColonyAlertsNotification -{ - public BehaviorNotification(Module owner) - { - super(owner); - } - - @Override - public String getName() - { - return "Behavior Notification"; - } - - @Override - public String getEmailSubject(Container c) - { - return "Behavior Alerts: " + getDateTimeFormat(c).format(new Date()); - } - - @Override - public String getCronString() - { - return "0 0 5 * * ?"; - } - - @Override - public String getScheduleDescription() - { - return "every day at 5:00AM"; - } - - @Override - public String getDescription() - { - return "The report is designed to provide a daily summary of issues related to behavior management, such as housing, pairing, and behavior cases"; - } - - @Override - public String getMessageBodyHTML(Container c, User u) - { - Map saved = getSavedValues(c); - Map toSave = new HashMap(); - - StringBuilder msg = new StringBuilder(); - - msg.append(getDescription()).append("
"); - - colonyHousingSummary(c, u, msg, saved, toSave); - behaviorCaseSummary(c, u, msg); - getFlaggedPairs(c, u, msg); - changedPairs(c, u, msg); - singleHousedAnimals(c, u, msg); - transfersYesterday(c, u, msg); - surgeryCasesRecentlyClosed(c, u, msg); - pairIdConflicts(c, u , msg); - NHPTraining_BehaviorAlert(c, u , msg); - dcmNotesAlert(c, u , msg); - - notesEndingToday(c, u, msg, Arrays.asList("BSU Notes"), null); - saveValues(c, toSave); - - return msg.toString(); - } - - // Added by Kollil 11/04/2020 - private void NHPTraining_BehaviorAlert(final Container c, User u, final StringBuilder msg) - { - if (QueryService.get().getUserSchema(u, c, "onprc_ehr") == null) { - msg.append("Warning: The onprc_ehr schema has not been enabled in this folder, so the alert cannot run!

"); - return; - } - TableInfo ti = QueryService.get().getUserSchema(u, c, "onprc_ehr").getTable("NHP_Training_BehaviorAlert",ContainerFilter.Type.AllFolders.create(c, u)); -// ((ContainerFilterable) ti).setContainerFilter(ContainerFilter.Type.AllFolders.create(u); - TableSelector ts = new TableSelector(ti, null, null); - - long total = ts.getRowCount(); - msg.append("NHP_Training entries where \"Training Result = In-Progress\" for over 60 days:

"); - if (total > 0) - { - msg.append("There are " + total + " entries found. "); - msg.append("

Click here to view them

\n"); - msg.append("
\n\n"); - } - else - { - msg.append("WARNING: There are no NHP_Training entries where \"Training Result = In Progress\" for over 60 days!
\n"); - } - - } - - /* - Kollil, Created: 11/18/20, Modified: 04/07/2021 - 1. New alert for DCM notes (category = notes pertaining to DAR) added the previous day. - 2. New alert for DCM notes (category = notes pertaining to DAR) removed the previous day. - 3. New alert for Flags added the previous day. - 4. New alert for Flags removed the previous day. - */ - /** - * Modified: 12-9-2021 R.Blasa using Lakshmi's original code - */ - protected void dcmNotesAlert(final Container c, User u, final StringBuilder msg) - { - SimpleFilter filter = new SimpleFilter(FieldKey.fromString("actiondate"), new Date(), CompareType.DATE_EQUAL); - filter.addCondition(FieldKey.fromString("category"), "Notes Pertaining to DAR", CompareType.EQUAL); - TableSelector ts = new TableSelector(getStudySchema(c, u).getTable("Notes_WithLocation"), filter, null); - long count = ts.getRowCount(); - if (count > 0) - { - msg.append("WARNING: There are " + count + " DCM action items.
\n"); - msg.append("

Click here to view them
\n\n"); - msg.append("


"); - } - else - { - msg.append("WARNING: There are no DCM action items!
"); - } - - //Added by Kollil on 11/04/2020 - //New alert for DCM notes (category = notes pertaining to DAR) added the previous day. - - //Get yesterday date - Calendar cal = Calendar.getInstance(); - cal.setTime(new Date()); - cal.add(Calendar.DATE, -1); - String formatted = getDateFormat(c).format(cal.getTime()); - - SimpleFilter filter1 = new SimpleFilter(FieldKey.fromString("date"), cal.getTime(), CompareType.DATE_EQUAL); - filter1.addCondition(FieldKey.fromString("category"), "Notes Pertaining to DAR", CompareType.EQUAL); - TableSelector ts1 = new TableSelector(getStudySchema(c, u).getTable("Notes_WithLocation"), filter1, null); - long count1 = ts1.getRowCount(); - msg.append("DCM Alerts:
"); - if (count1 > 0) { - msg.append("" + count1 + " DCM notes entries added yesterday where \"Category = Notes pertaining to DAR\".
\n"); - msg.append("

Click here to view them
\n\n"); - msg.append("


\n\n"); - } - else - { - msg.append("WARNING: No DCM notes added yesterday where \"Category = Notes pertaining to DAR\"!
"); - } - - /* Added by Kollil on 10/12/2023 - New alert for DCM notes (category = notes pertaining to DAR) removed the previous day. - Refer to tkt #9977 - */ - SimpleFilter filter4 = new SimpleFilter(FieldKey.fromString("enddate"), cal.getTime(), CompareType.DATE_EQUAL); - TableSelector ts4 = new TableSelector(getStudySchema(c, u).getTable("Notes_WithLocation"), filter4, null); - long count4 = ts4.getRowCount(); - - if (count4 > 0) { - msg.append("" + count4 + " DCM notes entries removed yesterday where \"Category = Notes pertaining to DAR\".
\n"); - msg.append("

Click here to view them
\n\n"); - msg.append("


\n\n"); - } - else { - msg.append("WARNING: No DCM notes ended yesterday where \"Category = Notes pertaining to DAR\"!
"); - } - - //Added by Kollil on 11/04/2020 - //New alert for Flags added the previous day. - SimpleFilter filter2 = new SimpleFilter(FieldKey.fromString("date"), cal.getTime(), CompareType.DATE_EQUAL); - TableSelector ts2 = new TableSelector(getStudySchema(c, u).getTable("Flags_WithLocation"), filter2, null); - long count2 = ts2.getRowCount(); - if (count2 > 0) - { - msg.append("There are " + count2 + " flag(s) added yesterday.
\n"); - msg.append("

Click here to view them
\n\n"); - msg.append("

"); - } - else - { - msg.append("WARNING: There are no flags added yesterday!
"); - } - - //Added by Kollil on 1/04/2021 - //New alert for Flags removed the previous day. - SimpleFilter filter3 = new SimpleFilter(FieldKey.fromString("enddate"), cal.getTime(), CompareType.DATE_EQUAL); - TableSelector ts3 = new TableSelector(getStudySchema(c, u).getTable("Flags_WithLocation"), filter3, null); - long count3 = ts3.getRowCount(); - if (count3 > 0) { - msg.append("" + count3 + " flag(s) removed yesterday.
\n"); - msg.append("

Click here to view them
\n\n"); - msg.append("

"); - } - else { - msg.append("WARNING: There are no flags removed yesterday!
"); - } - - } - - // Modified: 9-7-2018 R.Blasa - private void behaviorCaseSummary(Container c, User u, final StringBuilder msg) - { - TableInfo ti = getStudySchema(c, u).getTable("mostRecentObservationsBehavior"); - SimpleFilter filter = new SimpleFilter(FieldKey.fromString("isActive"), true); - - TableSelector ts = new TableSelector(ti, PageFlowUtil.set("Id"), filter, null); - long total = ts.getRowCount(); - msg.append("Behavior Cases:

"); - msg.append("There are " + total + " active behavior cases (this does not include cases closed for review). "); - String url = getExecuteQueryUrl(c, "study", "mostRecentObservationsBehavior", "Open Behavior Case") + "&query.isActive~eq=true"; - msg.append("Click here to view them"); - msg.append("

"); - } - - private void pairIdConflicts(Container c, User u, final StringBuilder msg) - { - TableInfo ti = getStudySchema(c, u).getTable("pairingIdConflicts"); - TableSelector ts = new TableSelector(ti); - long total = ts.getRowCount(); - if (total > 0) - { - msg.append("Conflicting Pair IDs:

"); - msg.append("There are " + total + " pairing records with conflicting pairIds. If this occurs, there is a bug in data entry which could cause unusual results when viewing the data. If you see this, please contact the site administrator. "); - String url = getExecuteQueryUrl(c, "study", "pairingIdConflicts", null); - msg.append("Click here to view them"); - msg.append("

"); - } - } - - private void singleHousedAnimals(Container c, User u, final StringBuilder msg) - { - TableInfo ti = getStudySchema(c, u).getTable("demographicsDaysAlone"); - SimpleFilter filter = new SimpleFilter(FieldKey.fromString("cagemates"), 0, CompareType.EQUAL); - filter.addCondition(FieldKey.fromString("daysAlone"), 30, CompareType.GT); - - TableSelector ts = new TableSelector(ti, PageFlowUtil.set("Id"), filter, null); - long total = ts.getRowCount(); - msg.append("Single Housed Animals:

"); - msg.append("There are " + total + " animals that have been single housed for at least 30 days. "); - String url = getExecuteQueryUrl(c, "study", "demographicsDaysAlone", null, filter) + "&query.sort=-DaysAlone"; - msg.append("Click here to view them"); - msg.append("

"); - } - - private void getFlaggedPairs(Container c, User u, final StringBuilder msg) - { - TableInfo ti = getStudySchema(c, u).getTable("pairingSeparations"); - TableSelector ts = new TableSelector(ti, PageFlowUtil.set("Id")); - long total = ts.getRowCount(); - if (total > 0) - { - msg.append("There are " + total + " animals with temporary separations, but there is no subsequent pairing observation to indicate a reunite, permanent separation, new pair formation, etc. These may need attention.

"); - String url = getExecuteQueryUrl(c, "study", "pairingSeparations", null); - msg.append("Click here to view them"); - msg.append("

"); - } - } - - private void changedPairs(Container c, User u, final StringBuilder msg) - { - Calendar date1 = Calendar.getInstance(); - date1.setTime(new Date()); - date1 = DateUtils.truncate(date1, Calendar.DATE); - - Calendar date2 = Calendar.getInstance(); - date2.setTime(new Date()); - date2 = DateUtils.truncate(date2, Calendar.DATE); - date2.add(Calendar.DATE, -1); - - UserSchema us = getStudySchema(c, u); - QueryDefinition qd = us.getQueryDefForTable("pairDifferences"); - List errors = new ArrayList<>(); - TableInfo ti = qd.getTable(us, errors, true); - Map params = new HashMap<>(); - params.put("Date1", date1.getTime()); - params.put("Date2", date2.getTime()); - - SQLFragment sql = ti.getFromSQL("t"); - QueryService.get().bindNamedParameters(sql, params); - - sql = new SQLFragment("SELECT * FROM " + sql.getSQL() + " WHERE (t.changeType IS NOT NULL AND t.changeType != 'Group Members Changed') ORDER BY ldk.naturalize(t.room1), ldk.naturalize(t.cage1)", sql.getParams()); - QueryService.get().bindNamedParameters(sql, params); - SqlSelector ss = new SqlSelector(ti.getSchema(), sql); - Collection> rows = ss.getMapCollection(); - - if (!rows.isEmpty()) - { - msg.append("There are " + rows.size() + " animals with differences in pairing since the previous day. Note, this considers full pairs vs. non-full pairs only (ie. grooming contact is treated as non-paired). It considers housing at midnight of the days in question. "); - String url = getExecuteQueryUrl(c, "study", "pairDifferences", null) + "&query.changeType~isnonblank&query.changeType~neq=Group Members Changed&query.param.Date1=" + getDateFormat(c).format(date1.getTime()) + "&query.param.Date2=" + getDateFormat(c).format(date2.getTime()); - - msg.append("Click here to view them

"); - - msg.append("

"); - msg.append(""); - - for (Map row : rows) - { - String animalUrl = getParticipantURL(c, (String)row.get("Id")); - msg.append(""); - } - - msg.append("
IdAnimals In CageCurrent RoomCurrent CageChange TypePrevious RoomPrevious CagePair Observations Entered On Date
" + row.get("Id") + "" + (row.get("animalsInCage1") == null ? "" : row.get("animalsInCage1")) + "" + row.get("room1") + "" + (row.get("cage1") == null ? "" : row.get("cage1")) + "" + row.get("changeType") + "" + (row.get("room2") == null ? "" : row.get("room2")) + "" + (row.get("cage2") == null ? "" : row.get("cage2")) + "" + row.get("pairObservations") + "
"); - } - else - { - msg.append("No pairs changed yesterday"); - } - - msg.append("
"); - } - - private void colonyHousingSummary(final Container c, User u, final StringBuilder msg, Map saved, Map toSave) - { - final String colonyHousingSummary = "colonyHousingSummary"; - final JSONObject oldValueMap = saved.containsKey(colonyHousingSummary) ? new JSONObject(saved.get(colonyHousingSummary)) : new JSONObject(); - final JSONObject newValueMap = new JSONObject(); - Date lastRunDate = saved.containsKey(lastSave) ? new Date(Long.parseLong(saved.get(lastSave))) : null; - - TableInfo ti = getStudySchema(c, u).getTable("housingPairingSummary"); - TableSelector ts = new TableSelector(ti, PageFlowUtil.set("category", "totalAnimals"), null, new Sort("category")); - msg.append("Housing summary:

"); - msg.append(""); - msg.append(""); - final String urlBase = getExecuteQueryUrl(c, "study", "demographics", "By Location"); - - ts.forEach(rs -> { - String category = rs.getString("category"); - msg.append(""); - - newValueMap.put(category, rs.getInt("totalAnimals")); - }); - - msg.append("
Category# AnimalsPrevious Value " + (lastRunDate == null ? "" : "(" + getDateFormat(c).format(lastRunDate) + ")") + "
").append(category).append("").append(rs.getInt("totalAnimals")).append(""); - if (oldValueMap.has(category)) - { - msg.append(oldValueMap.get(category)); - } - msg.append("
"); - msg.append("

"); - - toSave.put(colonyHousingSummary, newValueMap.toString()); - } -} diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/notification/TreatmentAlertsMPANotification.java b/onprc_ehr/src/org/labkey/onprc_ehr/notification/TreatmentAlertsMPANotification.java deleted file mode 100644 index 07e75a87d..000000000 --- a/onprc_ehr/src/org/labkey/onprc_ehr/notification/TreatmentAlertsMPANotification.java +++ /dev/null @@ -1,272 +0,0 @@ -/* - * Copyright (c) 2015-2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.onprc_ehr.notification; - -import org.apache.commons.lang3.time.DateUtils; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.Results; -import org.labkey.api.data.ResultsImpl; -import org.labkey.api.data.Selector; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; -import org.labkey.api.module.Module; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryService; -import org.labkey.api.security.User; -import org.labkey.api.ehr.notification.AbstractEHRNotification; -import org.labkey.api.util.PageFlowUtil; - -import java.sql.ResultSet; -import java.sql.SQLException; -import java.util.Calendar; -import java.util.Date; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Map; -import java.util.Set; -import java.util.TreeMap; - -//Added by Kollil 9/25/23 Post Op MPA injections scheduled at 2Pm on Wednesdays starting from Sep 13th, 2023 -//Tkt #9939 -public class TreatmentAlertsMPANotification extends AbstractEHRNotification -{ - public TreatmentAlertsMPANotification(Module owner) - { - super(owner); - } - - @Override - public String getName() - { - return "MPA Injection Alerts"; - } - - @Override - public String getDescription() - { - return "This runs every Wednesday at 2PM if there are MPA injections scheduled that have not yet been marked complete"; - } - - @Override - public String getEmailSubject(Container c) - { - return "MPA Injection Alert: " + getDateTimeFormat(c).format(new Date()); - } - - @Override - public String getCronString() { return "0 0 14 ? * WED * ";} - - @Override - public String getScheduleDescription() - { - return "Every Wednesday at 2PM"; - } - - @Override - public String getMessageBodyHTML(Container c, User u) - { - StringBuilder msg = new StringBuilder(); - - //Find today's date - Date now = new Date(); - msg.append("This email contains any treatments not marked as completed. It was run on: " + getDateFormat(c).format(now) + " at " + _timeFormat.format(now) + "

" + - "Please use the following contacts if the medication has not been completed.

" + - "Email: cmumedicationrequests@ohsu.edu
" + - "DCM Commons: 503 - 346 - 5074
" + - "Colony tech office: 503 - 346 - 5152
" + - "Colony hospital: 503 - 346 - 5424 " + "

"); - - processMPATreatments(c, u, msg, new Date()); - return msg.toString(); - } - - private void processMPATreatments(Container c, User u, final StringBuilder msg, final Date maxDate) - { - Date curDate = new Date(); - Date roundedMax = new Date(); - roundedMax.setTime(maxDate.getTime()); - roundedMax = DateUtils.truncate(roundedMax, Calendar.DATE); - - TableInfo ti = QueryService.get().getUserSchema(u, c, "study").getTable("treatmentScheduleMPA"); - - SimpleFilter filter = new SimpleFilter(FieldKey.fromString("date"), roundedMax, CompareType.DATE_EQUAL); - filter.addCondition(FieldKey.fromString("date"), maxDate, CompareType.LTE); - filter.addCondition(FieldKey.fromString("Id/DataSet/Demographics/calculated_status"), "Alive"); - - Set columns = new HashSet<>(); - columns.add(FieldKey.fromString("Id")); - columns.add(FieldKey.fromString("Id/curLocation/area")); - columns.add(FieldKey.fromString("Id/curLocation/room")); - columns.add(FieldKey.fromString("Id/curLoation/cage")); - columns.add(FieldKey.fromString("projectStatus")); - columns.add(FieldKey.fromString("treatmentStatus")); - columns.add(FieldKey.fromString("treatmentStatus/Label")); - columns.add(FieldKey.fromString("code")); - columns.add(FieldKey.fromString("code/meaning")); - - Map params = new HashMap<>(); - params.put("StartDate", roundedMax); - params.put("NumDays", 1); - - final Map colMap = QueryService.get().getColumns(ti, columns); - TableSelector ts = new TableSelector(ti, colMap.values(), filter, new Sort("Id/curLocation/area,Id/curLocation/room")); - ts.setNamedParameters(params); - - String url = getExecuteQueryUrl(c, "study", "treatmentScheduleMPA", null) + "&" + filter.toQueryString("query") + getParameterUrlString(c, params); - long total = ts.getRowCount(); - if (total == 0) { - msg.append("There are no MPA injections scheduled on " + getDateFormat(c).format(maxDate) + " on or before " + _timeFormat.format(maxDate) + ". Treatments could be added after this email was sent, so please click here to check online closer to the time.

\n"); - } - else { - final String completed = "completed"; - final String incomplete = "incomplete"; - final Map totals = new HashMap<>(); - totals.put(completed, 0); - totals.put(incomplete, 0); - - final Map totalByArea = new TreeMap<>(); - ts.forEach(new Selector.ForEachBlock() - { - @Override - public void exec(ResultSet object) throws SQLException { - Results rs = new ResultsImpl(object, colMap); - if ("Completed".equals(rs.getString(FieldKey.fromString("treatmentStatus")))) { - totals.put(completed, totals.get(completed) + 1); - } - else { - totals.put(incomplete, totals.get(incomplete) + 1); - - String area = rs.getString(FieldKey.fromString("Id/curLocation/area")); - Integer areaVal = totalByArea.containsKey(area) ? totalByArea.get(area) : 0; - areaVal++; - - totalByArea.put(area, areaVal); - } - } - }); - msg.append("Treatments:

"); - msg.append("There are " + (totals.get(completed) + totals.get(incomplete)) + " scheduled treatments on or before " + _timeFormat.format(maxDate) + ". Click here to view them. Of these, " + totals.get(completed) + " have been marked completed.

\n"); - - //////////////////////////////////////////////////////////////////////////////////////////////////////////// - //Add code to display report, by Kollil - - TableInfo ti1 = QueryService.get().getUserSchema(u, c, "study").getTable("treatmentScheduleMPA"); - - //All fields - Set columns1 = new HashSet<>(); - columns1.add(FieldKey.fromString("id")); - columns1.add(FieldKey.fromString("calculated_status")); - columns1.add(FieldKey.fromString("treatmentStatus")); - columns1.add(FieldKey.fromString("room")); - columns1.add(FieldKey.fromString("cage")); - columns1.add(FieldKey.fromString("date")); - columns1.add(FieldKey.fromString("startDate")); - columns1.add(FieldKey.fromString("endDate")); - columns1.add(FieldKey.fromString("dayselapsed")); - columns1.add(FieldKey.fromString("category")); - columns1.add(FieldKey.fromString("medication")); - columns1.add(FieldKey.fromString("volume")); - columns1.add(FieldKey.fromString("vol_units")); - columns1.add(FieldKey.fromString("concentration")); - columns1.add(FieldKey.fromString("conc_units")); - columns1.add(FieldKey.fromString("amountWithUnits")); - columns1.add(FieldKey.fromString("amountAndVolume")); - columns1.add(FieldKey.fromString("dosage")); - columns1.add(FieldKey.fromString("dosage_units")); - columns1.add(FieldKey.fromString("frequency")); - columns1.add(FieldKey.fromString("route")); - columns1.add(FieldKey.fromString("reason")); - columns1.add(FieldKey.fromString("remark")); - columns1.add(FieldKey.fromString("performedby")); - - final Map colMap1 = QueryService.get().getColumns(ti1, columns1); - TableSelector ts1 = new TableSelector(ti1, colMap1.values(), filter, new Sort("id")); - ts1.setNamedParameters(params); - total = ts1.getRowCount(); - - if (total == 0) { - msg.append("There are no MPA injections."); - } - else { - msg.append("


MPA Injections:

\n"); - msg.append(""); - msg.append(""); - - ts1.forEach(new Selector.ForEachBlock() - { - @Override - public void exec(ResultSet object) throws SQLException - { - Results rs = new ResultsImpl(object, colMap1); - String status = rs.getString("TreatmentStatus"); - if ("completed".equalsIgnoreCase(status)) { - msg.append(""); - } - else { - //If not "completed", highlight the record with yellow color - msg.append(""); - } - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - msg.append(""); - } - }); - - msg.append("
IdStatusTreatment StatusRoomCageTreatment DateTreatment Start DateTreatment End DateDays ElapsedCategoryTreatmentVolumeVolume UnitsDrug ConcConc UnitsAmountAmount And VolumeDosageDosage UnitsFrequencyRouteReasonRemarkOrdered By
" + PageFlowUtil.filter(rs.getString("id")) + "" + PageFlowUtil.filter(rs.getString("calculated_status")) + "" + PageFlowUtil.filter(rs.getString("TreatmentStatus")) + "" + PageFlowUtil.filter(rs.getString("room")) + "" + PageFlowUtil.filter(rs.getString("cage")) + "" + PageFlowUtil.filter(rs.getString("date")) + "" + PageFlowUtil.filter(rs.getString("startDate")) + "" + PageFlowUtil.filter(rs.getString("endDate")) + "" + PageFlowUtil.filter(rs.getString("dayselapsed")) + "" + PageFlowUtil.filter(rs.getString("category")) + "" + PageFlowUtil.filter(rs.getString("medication")) + "" + PageFlowUtil.filter(rs.getString("volume")) + "" + PageFlowUtil.filter(rs.getString("vol_units")) + "" + PageFlowUtil.filter(rs.getString("concentration")) + "" + PageFlowUtil.filter(rs.getString("conc_units")) + "" + PageFlowUtil.filter(rs.getString("amountWithUnits")) + "" + PageFlowUtil.filter(rs.getString("amountAndVolume")) + "" + PageFlowUtil.filter(rs.getString("dosage")) + "" + PageFlowUtil.filter(rs.getString("dosage_units")) + "" + PageFlowUtil.filter(rs.getString("frequency")) + "" + PageFlowUtil.filter(rs.getString("route")) + "" + PageFlowUtil.filter(rs.getString("reason")) + "" + PageFlowUtil.filter(rs.getString("remark")) + "" + PageFlowUtil.filter(rs.getString("performedby")) + "
"); - } - //////////////////////////////////////////////////////////////////////////////////////////////////////// - if (totals.get(incomplete) == 0) { - msg.append("All MPA medications scheduled prior to " + _timeFormat.format(maxDate) + " have been marked complete as of " + getDateTimeFormat(c).format(curDate) + ".

\n"); - } - else { - msg.append("There are " + totals.get(incomplete) + " treatments that have not been marked complete:

\n"); - msg.append(""); - for (String area : totalByArea.keySet()) - { - msg.append("\n"); - } - msg.append("
" + area + ":" + totalByArea.get(area) + "

\n"); - } - msg.append("

\n"); - } - } -} \ No newline at end of file