From ec49906bacb30d76970fd97f4f2295198433e374 Mon Sep 17 00:00:00 2001 From: Lakshmi Kolli <69940873+kollil@users.noreply.github.com> Date: Mon, 11 Nov 2024 10:08:03 -0800 Subject: [PATCH] Pathology assignments alert (#1173) * Created a new alert to report any animal assignments where projected release condition is terminal in the last 35 days. * Updated the center project display. * Updated the display fields on the report Updated the cron job time --- .../study/pathAssignmentData.query.xml | 9 + .../queries/study/pathAssignmentData.sql | 21 +++ .../org/labkey/onprc_ehr/ONPRC_EHRModule.java | 3 + .../PathAssignmentNotification.java | 160 ++++++++++++++++++ 4 files changed, 193 insertions(+) create mode 100644 onprc_ehr/resources/queries/study/pathAssignmentData.query.xml create mode 100644 onprc_ehr/resources/queries/study/pathAssignmentData.sql create mode 100644 onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java diff --git a/onprc_ehr/resources/queries/study/pathAssignmentData.query.xml b/onprc_ehr/resources/queries/study/pathAssignmentData.query.xml new file mode 100644 index 000000000..ad055e69c --- /dev/null +++ b/onprc_ehr/resources/queries/study/pathAssignmentData.query.xml @@ -0,0 +1,9 @@ + + + + + Assignments for Pathology +
+ + + diff --git a/onprc_ehr/resources/queries/study/pathAssignmentData.sql b/onprc_ehr/resources/queries/study/pathAssignmentData.sql new file mode 100644 index 000000000..66f5c17c8 --- /dev/null +++ b/onprc_ehr/resources/queries/study/pathAssignmentData.sql @@ -0,0 +1,21 @@ +SELECT Id, +-- Id.demographics.gender as Sex, + CASE + WHEN Id.demographics.gender = 'F' THEN 'Female' + WHEN Id.demographics.gender = 'M' THEN 'Male' + ELSE 'Unknown' + END AS Sex, + Id.Age.ageinyearsrounded as AgeInYearsRounded, + project.name as project, + project.protocol.investigatorId.lastname as Investigator, + project.title as Title, + date, + enddate, + projectedRelease, + (Select meaning from ehr_lookups.animal_condition where code = assignment.projectedReleaseCondition) as projectedReleaseCondition, + (Select meaning from ehr_lookups.animal_condition where code = assignment.assignCondition) as assignCondition, + (Select meaning from ehr_lookups.animal_condition where code = assignment.releaseCondition) as releaseCondition, +FROM assignment +Where projectedReleaseCondition = 206 --'Terminal' +And date <= curdate() and date >= timestampadd(SQL_TSI_DAY, -35, curdate()) + 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 ff06b7cd2..df0f81a3f 100644 --- a/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java +++ b/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java @@ -225,6 +225,9 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext) //Added Aug 9th, 2024 Kollil ns.registerNotification(new AdminNotifications(this)); + //Added Nov 5th, 2024 Kollil + ns.registerNotification(new PathAssignmentNotification(this)); + //Added 8-7-2018 R.Blasa ns.registerNotification(new BirthHousingMismatchNotification(this)); diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java b/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java new file mode 100644 index 000000000..82df2695a --- /dev/null +++ b/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java @@ -0,0 +1,160 @@ +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.ContainerFilter; +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.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; + +/** + * Created by kollil on 10/24/2019. + */ + +public class PathAssignmentNotification extends ColonyAlertsNotification +{ + public PathAssignmentNotification(Module owner) + { + super(owner); + } + + @Override + public String getName() + { + return "Pathology Assignemnt Notification"; + } + + @Override + public String getEmailSubject(Container c) + { + return "Animal assignment alerts for Pathology: " + getDateTimeFormat(c).format(new Date()); + } + + @Override + public String getCronString() + { + return "0 0 9 ? * MON"; + + } + + @Override + public String getScheduleDescription() + { + return "every Monday at 9Am"; + } + + @Override + public String getDescription() + { + return "The report is designed to send animal assignments data to pathology every Monday!"; + } + + @Override + public String getMessageBodyHTML(Container c, User u) + { + StringBuilder msg = new StringBuilder(); + + pathAssignmentAlert(c, u, msg); + + return msg.toString(); + } + + /** + * Kollil, 11/05/2024 : Ticket # 11319, listing assignments made with release condition as 'terminal' with the anticipated release date. It could look something like this: + * a. Query: Assignment date = within the last 35 days, with 'projected release condition' = Terminal + * b. Report: Table with columns as attached (I created a custom view as an example, but you can include whatever info is relevant) + **/ + private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) + { + if (QueryService.get().getUserSchema(u, c, "study") == null) + { + msg.append("Warning: The study schema has not been enabled in this folder, so the alert cannot run!

"); + return; + } + //assignments query + TableInfo ti = QueryService.get().getUserSchema(u, c, "study").getTable("pathAssignmentData", ContainerFilter.Type.AllFolders.create(c, u)); + TableSelector ts = new TableSelector(ti, null, null); + long count = ts.getRowCount(); + + //Get num of rows + if (count > 0) + { + msg.append("" + count + " assignments found with projected release condition = Terminal in the last 35 days:"); + msg.append("

Click here to view the assignments in PRIME

\n"); + msg.append("
"); + } + else + { + msg.append(" There are no assignments found with projected release condition = Terminal in the last 35 days "); + msg.append("
"); + } + + //Display the daily report in the email + if (count > 0) + { + Set columns = new HashSet<>(); + columns.add(FieldKey.fromString("Id")); + columns.add(FieldKey.fromString("Sex")); + columns.add(FieldKey.fromString("AgeInYearsRounded")); + columns.add(FieldKey.fromString("project")); + columns.add(FieldKey.fromString("Investigator")); + columns.add(FieldKey.fromString("Title")); + columns.add(FieldKey.fromString("date")); + columns.add(FieldKey.fromString("enddate")); + columns.add(FieldKey.fromString("projectedRelease")); + columns.add(FieldKey.fromString("projectedReleaseCondition")); + columns.add(FieldKey.fromString("assignCondition")); + columns.add(FieldKey.fromString("releaseCondition")); + + final Map colMap = QueryService.get().getColumns(ti, columns); + TableSelector ts2 = new TableSelector(ti, colMap.values(), null, null); + + msg.append("
Assignments:

\n"); + msg.append(""); + msg.append(""); + msg.append(""); + + ts2.forEach(object -> { + Results rs = new ResultsImpl(object, colMap); + String url = getParticipantURL(c, rs.getString("Id")); + + msg.append(""); + msg.append("\n"); + 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("
Id Sex Age (Years, Rounded) Center Project Investigator Title Assign Date Release Date Projected Release Date Projected Release Condition Condition At Assignment Condition At Release
" + PageFlowUtil.filter(rs.getString("Id")) + " " + PageFlowUtil.filter(rs.getString("Sex")) + "" + PageFlowUtil.filter(rs.getString("AgeInYearsRounded")) + "" + PageFlowUtil.filter(rs.getString("project")) + "" + PageFlowUtil.filter(rs.getString("Investigator")) + "" + PageFlowUtil.filter(rs.getString("Title")) + "" + PageFlowUtil.filter(rs.getString("date")) + "" + PageFlowUtil.filter(rs.getString("enddate")) + "" + PageFlowUtil.filter(rs.getString("projectedRelease")) + "" + PageFlowUtil.filter(rs.getString("projectedReleaseCondition")) + "" + PageFlowUtil.filter(rs.getString("assigncondition")) + "" + PageFlowUtil.filter(rs.getString("releasecondition")) + "
"); + } + } +}