From d3507ba197bc116ae7aebb1e3137317e877754f5 Mon Sep 17 00:00:00 2001 From: kollil Date: Tue, 5 Nov 2024 15:13:21 -0800 Subject: [PATCH 1/3] Created a new alert to report any animal assignments where projected release condition is terminal in the last 35 days. --- .../study/pathAssignmentData.query.xml | 9 + .../queries/study/pathAssignmentData.sql | 16 ++ .../org/labkey/onprc_ehr/ONPRC_EHRModule.java | 3 + .../PathAssignmentNotification.java | 160 ++++++++++++++++++ 4 files changed, 188 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..10ced6432 --- /dev/null +++ b/onprc_ehr/resources/queries/study/pathAssignmentData.sql @@ -0,0 +1,16 @@ +SELECT Id, + project, + date, + projectedRelease, + enddate, + assignmentType, + (Select meaning from ehr_lookups.animal_condition where code = assignment.assignCondition) as assignCondition, + (Select meaning from ehr_lookups.animal_condition where code = assignment.projectedReleaseCondition) as projectedReleaseCondition, + (Select meaning from ehr_lookups.animal_condition where code = assignment.releaseCondition) as releaseCondition, + releaseType, + remark, + description +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..af80c1484 --- /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 30 7 ? * MON"; + + } + + @Override + public String getScheduleDescription() + { + return "every Monday at 7:30Am"; + } + + @Override + public String getDescription() + { + return "The report is designed to send animal assignments data to pathology every other 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; + } + //Fasts 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("project")); + columns.add(FieldKey.fromString("date")); + columns.add(FieldKey.fromString("projectedRelease")); + columns.add(FieldKey.fromString("enddate")); + columns.add(FieldKey.fromString("assignmentType")); + columns.add(FieldKey.fromString("assignCondition")); + columns.add(FieldKey.fromString("projectedReleaseCondition")); + columns.add(FieldKey.fromString("releaseCondition")); + columns.add(FieldKey.fromString("releaseType")); + columns.add(FieldKey.fromString("remark")); + columns.add(FieldKey.fromString("description")); + + 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 Center Project Assign Date Projected Release Date Release Date Assignment Type Condition At Assignment Projected Release Condition Condition At Release Release Type Remark Description
" + PageFlowUtil.filter(rs.getString("Id")) + " " + PageFlowUtil.filter(rs.getString("project")) + "" + PageFlowUtil.filter(rs.getString("date")) + "" + PageFlowUtil.filter(rs.getString("projectedRelease")) + "" + PageFlowUtil.filter(rs.getString("enddate")) + "" + PageFlowUtil.filter(rs.getString("assignmentType")) + "" + PageFlowUtil.filter(rs.getString("assignCondition")) + "" + PageFlowUtil.filter(rs.getString("projectedReleaseCondition")) + "" + PageFlowUtil.filter(rs.getString("releaseCondition")) + "" + PageFlowUtil.filter(rs.getString("releaseType")) + "" + PageFlowUtil.filter(rs.getString("remark")) + "" + PageFlowUtil.filter(rs.getString("description")) + "
"); + } + } +} From 2f54117d6fb2671a974994aea9a628f9f503de90 Mon Sep 17 00:00:00 2001 From: kollil Date: Wed, 6 Nov 2024 12:54:21 -0800 Subject: [PATCH 2/3] Updated the center project display. --- onprc_ehr/resources/queries/study/pathAssignmentData.sql | 2 +- .../notification/PathAssignmentNotification.java | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/onprc_ehr/resources/queries/study/pathAssignmentData.sql b/onprc_ehr/resources/queries/study/pathAssignmentData.sql index 10ced6432..433ce5f03 100644 --- a/onprc_ehr/resources/queries/study/pathAssignmentData.sql +++ b/onprc_ehr/resources/queries/study/pathAssignmentData.sql @@ -1,5 +1,5 @@ SELECT Id, - project, + project.name as project, date, projectedRelease, enddate, diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java b/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java index af80c1484..153879a53 100644 --- a/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java +++ b/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java @@ -67,7 +67,7 @@ public String getScheduleDescription() @Override public String getDescription() { - return "The report is designed to send animal assignments data to pathology every other Monday!"; + return "The report is designed to send animal assignments data to pathology every Monday!"; } @Override @@ -125,7 +125,7 @@ private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) columns.add(FieldKey.fromString("releaseCondition")); columns.add(FieldKey.fromString("releaseType")); columns.add(FieldKey.fromString("remark")); - columns.add(FieldKey.fromString("description")); +// columns.add(FieldKey.fromString("description")); final Map colMap = QueryService.get().getColumns(ti, columns); TableSelector ts2 = new TableSelector(ti, colMap.values(), null, null); @@ -133,7 +133,7 @@ private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) msg.append("
Assignments:

\n"); msg.append(""); msg.append(""); - msg.append(""); + msg.append(""); ts2.forEach(object -> { Results rs = new ResultsImpl(object, colMap); @@ -151,7 +151,7 @@ private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) msg.append(""); msg.append(""); msg.append(""); - msg.append(""); +// msg.append(""); msg.append(""); }); msg.append("
Id Center Project Assign Date Projected Release Date Release Date Assignment Type Condition At Assignment Projected Release Condition Condition At Release Release Type Remark Description
Id Center Project Assign Date Projected Release Date Release Date Assignment Type Condition At Assignment Projected Release Condition Condition At Release Release Type Remark
" + PageFlowUtil.filter(rs.getString("releaseCondition")) + "" + PageFlowUtil.filter(rs.getString("releaseType")) + "" + PageFlowUtil.filter(rs.getString("remark")) + "" + PageFlowUtil.filter(rs.getString("description")) + "" + PageFlowUtil.filter(rs.getString("description")) + "
"); From b6d6a1cf435c824d4b9a9d9a3f35127298345202 Mon Sep 17 00:00:00 2001 From: kollil Date: Thu, 7 Nov 2024 14:52:32 -0800 Subject: [PATCH 3/3] Updated the display fields on the report Updated the cron job time --- .../queries/study/pathAssignmentData.sql | 17 ++++++---- .../PathAssignmentNotification.java | 34 +++++++++---------- 2 files changed, 28 insertions(+), 23 deletions(-) diff --git a/onprc_ehr/resources/queries/study/pathAssignmentData.sql b/onprc_ehr/resources/queries/study/pathAssignmentData.sql index 433ce5f03..66f5c17c8 100644 --- a/onprc_ehr/resources/queries/study/pathAssignmentData.sql +++ b/onprc_ehr/resources/queries/study/pathAssignmentData.sql @@ -1,15 +1,20 @@ 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, - projectedRelease, enddate, - assignmentType, - (Select meaning from ehr_lookups.animal_condition where code = assignment.assignCondition) as assignCondition, + 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, - releaseType, - remark, - description 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/notification/PathAssignmentNotification.java b/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java index 153879a53..82df2695a 100644 --- a/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java +++ b/onprc_ehr/src/org/labkey/onprc_ehr/notification/PathAssignmentNotification.java @@ -54,14 +54,14 @@ public String getEmailSubject(Container c) @Override public String getCronString() { - return "0 30 7 ? * MON"; + return "0 0 9 ? * MON"; } @Override public String getScheduleDescription() { - return "every Monday at 7:30Am"; + return "every Monday at 9Am"; } @Override @@ -92,7 +92,7 @@ private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) msg.append("Warning: The study schema has not been enabled in this folder, so the alert cannot run!

"); return; } - //Fasts query + //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(); @@ -115,17 +115,17 @@ private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) { 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("projectedRelease")); columns.add(FieldKey.fromString("enddate")); - columns.add(FieldKey.fromString("assignmentType")); - columns.add(FieldKey.fromString("assignCondition")); + columns.add(FieldKey.fromString("projectedRelease")); columns.add(FieldKey.fromString("projectedReleaseCondition")); + columns.add(FieldKey.fromString("assignCondition")); columns.add(FieldKey.fromString("releaseCondition")); - columns.add(FieldKey.fromString("releaseType")); - columns.add(FieldKey.fromString("remark")); -// columns.add(FieldKey.fromString("description")); final Map colMap = QueryService.get().getColumns(ti, columns); TableSelector ts2 = new TableSelector(ti, colMap.values(), null, null); @@ -133,7 +133,7 @@ private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) msg.append("
Assignments:

\n"); msg.append(""); msg.append(""); - msg.append(""); + msg.append(""); ts2.forEach(object -> { Results rs = new ResultsImpl(object, colMap); @@ -141,17 +141,17 @@ private void pathAssignmentAlert(Container c, User u, final StringBuilder msg) 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(""); - msg.append(""); - msg.append(""); -// msg.append(""); + msg.append(""); + msg.append(""); msg.append(""); }); msg.append("
Id Center Project Assign Date Projected Release Date Release Date Assignment Type Condition At Assignment Projected Release Condition Condition At Release Release Type Remark
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("projectedRelease")) + "" + PageFlowUtil.filter(rs.getString("enddate")) + "" + PageFlowUtil.filter(rs.getString("assignmentType")) + "" + PageFlowUtil.filter(rs.getString("assignCondition")) + "" + PageFlowUtil.filter(rs.getString("projectedRelease")) + "" + PageFlowUtil.filter(rs.getString("projectedReleaseCondition")) + "" + PageFlowUtil.filter(rs.getString("releaseCondition")) + "" + PageFlowUtil.filter(rs.getString("releaseType")) + "" + PageFlowUtil.filter(rs.getString("remark")) + "" + PageFlowUtil.filter(rs.getString("description")) + "" + PageFlowUtil.filter(rs.getString("assigncondition")) + "" + PageFlowUtil.filter(rs.getString("releasecondition")) + "
");