From 74d287e3821dbbf13610ac7994800293f19ca17a Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 6 Oct 2020 13:39:17 -0700 Subject: [PATCH 01/34] Merge from onprc19.1 r.63271 --- .../completionDates/.qview.xml | 1 + .../EHR_ComplianceDB-12.38-12.39.sql | 1 + .../EHR_ComplianceDB-12.38-12.39.sql | 1 + .../resources/schemas/ehr_compliancedb.xml | 8 +++ .../EHR_ComplianceDBModule.java | 2 +- .../org/labkey/api/ehr/EHRService.java | 32 ++++++++- .../labkey/api/ehr/history/LabworkType.java | 5 ++ .../labkey/api/ehr/table/DurationColumn.java | 67 ++++++++++++------- ehr/resources/views/groupOverlaps.html | 10 ++- ehr/resources/views/housingOverlaps.html | 2 +- ehr/resources/web/ehr/DataEntryUtils.js | 11 ++- ehr/resources/web/ehr/grid/Panel.js | 21 ++++-- .../web/ehr/model/sources/Default.js | 18 +++++ .../web/ehr/panel/AnimalGroupDetailsPanel.js | 2 +- .../web/ehr/panel/ClinicalManagementPanel.js | 3 +- ehr/resources/web/ehr/utils.js | 4 +- .../web/ehr/window/CreateTaskFromIdsWindow.js | 4 +- .../ehr/window/CreateTaskFromRecordsWindow.js | 4 +- .../ehr/window/EncounterAddRecordWindow.js | 2 +- ehr/src/org/labkey/ehr/EHRModule.java | 3 + ehr/src/org/labkey/ehr/EHRServiceImpl.java | 3 +- .../ehr/history/ClinicalHistoryManager.java | 20 ++++-- .../ehr/history/DefaultLabworkDataSource.java | 14 ++-- .../labkey/ehr/history/LabworkManager.java | 13 ++++ .../security/EHRProtocolManagementRole.java | 3 +- .../ehr/table/AbstractAgeDisplayColumn.java | 13 ++++ .../labkey/ehr/table/AgeDisplayColumn.java | 15 +---- .../ehr/table/AgeMonthsDisplayColumn.java | 17 ++--- .../ehr/table/AgeYearMonthsDisplayColumn.java | 15 +---- .../AgeYearsMonthsDaysDisplayColumn.java | 15 +---- .../ehr/table/DefaultEHRCustomizer.java | 41 +++++++++--- .../labkey/ehr/utils/TriggerScriptHelper.java | 34 ++++++++-- 32 files changed, 275 insertions(+), 129 deletions(-) create mode 100644 EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.38-12.39.sql create mode 100644 EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.38-12.39.sql create mode 100644 ehr/src/org/labkey/ehr/table/AbstractAgeDisplayColumn.java diff --git a/EHR_ComplianceDB/resources/queries/ehr_compliancedb/completionDates/.qview.xml b/EHR_ComplianceDB/resources/queries/ehr_compliancedb/completionDates/.qview.xml index 0a2d166f1..98bc8263f 100644 --- a/EHR_ComplianceDB/resources/queries/ehr_compliancedb/completionDates/.qview.xml +++ b/EHR_ComplianceDB/resources/queries/ehr_compliancedb/completionDates/.qview.xml @@ -22,6 +22,7 @@ + diff --git a/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.38-12.39.sql b/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.38-12.39.sql new file mode 100644 index 000000000..230b83b76 --- /dev/null +++ b/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.38-12.39.sql @@ -0,0 +1 @@ +ALTER TABLE ehr_compliancedb.CompletionDates ADD COLUMN FileName varchar(500); \ No newline at end of file diff --git a/EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.38-12.39.sql b/EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.38-12.39.sql new file mode 100644 index 000000000..ca7d99334 --- /dev/null +++ b/EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.38-12.39.sql @@ -0,0 +1 @@ +ALTER TABLE ehr_compliancedb.CompletionDates ADD FileName nvarchar(500); \ No newline at end of file diff --git a/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml b/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml index 987fd4062..6549d3634 100644 --- a/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml +++ b/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml @@ -201,10 +201,12 @@ true Start Date + Date true End Date + Date true @@ -511,6 +513,7 @@ false Date Completed + Date true @@ -529,6 +532,10 @@ true Comment + + FileName + false + false true @@ -709,6 +716,7 @@ true Date Completed + Date false diff --git a/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java b/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java index 766116000..d3d390318 100644 --- a/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java +++ b/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java @@ -49,7 +49,7 @@ public String getName() @Override public @Nullable Double getSchemaVersion() { - return 12.38; + return 12.39; } @Override diff --git a/ehr/api-src/org/labkey/api/ehr/EHRService.java b/ehr/api-src/org/labkey/api/ehr/EHRService.java index 923215310..9f3d998bc 100644 --- a/ehr/api-src/org/labkey/api/ehr/EHRService.java +++ b/ehr/api-src/org/labkey/api/ehr/EHRService.java @@ -19,6 +19,8 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.AbstractTableInfo; import org.labkey.api.data.Container; +import org.labkey.api.data.CoreSchema; +import org.labkey.api.data.SQLFragment; import org.labkey.api.data.TableCustomizer; import org.labkey.api.data.TableInfo; import org.labkey.api.ehr.dataentry.DataEntryForm; @@ -26,12 +28,12 @@ import org.labkey.api.ehr.dataentry.SingleQueryFormProvider; import org.labkey.api.ehr.demographics.DemographicsProvider; import org.labkey.api.ehr.demographics.ProjectValidator; -import org.labkey.api.ehr.history.HistoryDataSource; -import org.labkey.api.ehr.history.LabworkType; +import org.labkey.api.ehr.history.*; import org.labkey.api.ldk.table.ButtonConfigFactory; import org.labkey.api.module.Module; import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.DetailsURL; +import org.labkey.api.query.ExprColumn; import org.labkey.api.query.FieldKey; import org.labkey.api.resource.Resource; import org.labkey.api.security.User; @@ -126,6 +128,32 @@ static public void setInstance(EHRService instance) /** @return the project validator set by the EHR module, note a center specific module may have overridden the default */ abstract public ProjectValidator getProjectValidator(); + public enum EndingOption + { + /** end date is not set, or any day in the future */ + activeAfterMidnightTonight(new SQLFragment(" WHEN (CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) > {fn curdate()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE())), + /** ends anytime today */ + endsToday(new SQLFragment("WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NOT NULL AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) = {fn curdate()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE())), + /** consider records that start/stop on today's date to be active */ + allowSameDay(new SQLFragment(" WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NOT NULL AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) = {fn curdate()} AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".date as DATE) = {fn curdate()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE())), + /** end time must be before right now */ + endingBeforeNow(new SQLFragment(" WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate >= {fn now()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE())); + + private final SQLFragment _sql; + + EndingOption(SQLFragment sql) + { + _sql = sql; + } + + public SQLFragment getSql() + { + return _sql; + } + } + + public abstract void addIsActiveCol(AbstractTableInfo ti, boolean includeExpired, EndingOption... endOptions); + /** Categories where pre-configured reports can be offered to the user */ public enum REPORT_LINK_TYPE { diff --git a/ehr/api-src/org/labkey/api/ehr/history/LabworkType.java b/ehr/api-src/org/labkey/api/ehr/history/LabworkType.java index 0ab6413d9..f864cd3aa 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/LabworkType.java +++ b/ehr/api-src/org/labkey/api/ehr/history/LabworkType.java @@ -39,4 +39,9 @@ public interface LabworkType Map> getResults(Container c, User u, List runIds, boolean redacted); Map> getResults(Container c, User u, String id, Date minDate, Date maxDate, boolean redacted); + + default boolean showPerformedBy() + { + return true; + } } diff --git a/ehr/api-src/org/labkey/api/ehr/table/DurationColumn.java b/ehr/api-src/org/labkey/api/ehr/table/DurationColumn.java index 0d27ffc05..44bad57c3 100644 --- a/ehr/api-src/org/labkey/api/ehr/table/DurationColumn.java +++ b/ehr/api-src/org/labkey/api/ehr/table/DurationColumn.java @@ -17,6 +17,7 @@ import org.apache.commons.lang3.time.DurationFormatUtils; import org.jetbrains.annotations.NotNull; +import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DataColumn; import org.labkey.api.data.RenderContext; @@ -32,9 +33,11 @@ public class DurationColumn extends DataColumn { - String _startDateColumn; - String _endDateColumn; - private String _durationFormat; + protected final String _startDateColumn; + protected final String _endDateColumn; + private final String _durationFormat; + + private boolean _dropTime; public DurationColumn(ColumnInfo col, String startDateColumn, String endDateColumn) { @@ -49,6 +52,12 @@ public DurationColumn(ColumnInfo col, String startDateColumn, String endDateColu _durationFormat = durationFormat; } + /** Treat all times as if they were at midnight of the same day */ + public void setDropTime(boolean dropTime) + { + _dropTime = dropTime; + } + @Override public Class getDisplayValueClass() { @@ -60,12 +69,24 @@ public Class getDisplayValueClass() @Override public Object getDisplayValue(RenderContext ctx) { - return getFormattedDuration((Date)ctx.get(getMappedFieldKey(_startDateColumn)), (Date)ctx.get(getMappedFieldKey(_endDateColumn))); + Date startDate = (Date)ctx.get(getMappedFieldKey(_startDateColumn)); + Date endDate = (Date)ctx.get(getMappedFieldKey(_endDateColumn)); + + return getFormattedDuration(startDate, endDate); + } + + private void dropTime(@NotNull Calendar cal) + { + cal.set(Calendar.HOUR_OF_DAY, 0); + cal.set(Calendar.MINUTE, 0); + cal.set(Calendar.SECOND, 0); + cal.set(Calendar.MILLISECOND, 0); } - protected String getFormattedDuration(Date startDate, Date endDate) + /** Convert from dates to calendars, dealing with nulls */ + public final String getFormattedDuration(@Nullable Date startDate, @Nullable Date endDate) { - if (startDate == null || _durationFormat == null) + if (startDate == null) return null; Calendar startCal = Calendar.getInstance(); @@ -74,6 +95,20 @@ protected String getFormattedDuration(Date startDate, Date endDate) Calendar endCal = Calendar.getInstance(); endCal.setTime(endDate == null ? new Date() : endDate); + if (_dropTime) + { + // Snap to midnight so that days work based on calendar day instead of 24-hour periods + dropTime(startCal); + dropTime(endCal); + } + return getFormattedDuration(startCal, endCal); + } + + protected String getFormattedDuration(@NotNull Calendar startCal, @NotNull Calendar endCal) + { + if (_durationFormat == null) + return null; + String formattedDuration; try { @@ -113,24 +148,4 @@ protected FieldKey getMappedFieldKey(String colName) { return new FieldKey(getBoundColumn().getFieldKey().getParent(), colName); } - - public String getStartDateColumn() - { - return _startDateColumn; - } - - public void setStartDateColumn(String startDateColumn) - { - _startDateColumn = startDateColumn; - } - - public String getEndDateColumn() - { - return _endDateColumn; - } - - public void setEndDateColumn(String endDateColumn) - { - _endDateColumn = endDateColumn; - } } diff --git a/ehr/resources/views/groupOverlaps.html b/ehr/resources/views/groupOverlaps.html index cf8e4bcb3..2f329e23c 100644 --- a/ehr/resources/views/groupOverlaps.html +++ b/ehr/resources/views/groupOverlaps.html @@ -154,7 +154,7 @@ renderTo: this.qwpDiv.id, schemaName: 'study', queryName: queryName, - title: 'Group Members' + title: 'Group Members Test', }; if (!start){ @@ -162,8 +162,11 @@ return; } + // By Kollil, 3/22/2018 : In 17.2 the filter is not working. Removed the the line 168 and added the filterArray at line 169. + // The Animal group search is working fine now after this change. if (groupName) - config.removeableFilters = [LABKEY.Filter.create('groupId/name', groupName, LABKEY.Filter.Types.EQUAL)]; + //config.removeableFilters = [LABKEY.Filter.create('groupId/name', groupName, LABKEY.Filter.Types.EQUAL)]; + config.filterArray = [LABKEY.Filter.create('groupId/name', groupName, LABKEY.Filter.Types.EQUAL)]; var params = { StartDate: start, @@ -172,7 +175,8 @@ config.parameters = params; - LDK.Utils.getReadOnlyQWP(config).render(this.qwpDiv.id); + LDK.Utils.getReadOnlyQWP(config); + } }); diff --git a/ehr/resources/views/housingOverlaps.html b/ehr/resources/views/housingOverlaps.html index 4122230f2..bb691f629 100644 --- a/ehr/resources/views/housingOverlaps.html +++ b/ehr/resources/views/housingOverlaps.html @@ -200,7 +200,7 @@ if (!LABKEY.Utils.isEmptyObj(params)) config.parameters = params; - LDK.Utils.getReadOnlyQWP(config).render(this.qwpDiv.id); + LDK.Utils.getReadOnlyQWP(config); } }).render(webpart.wrapperDivId); diff --git a/ehr/resources/web/ehr/DataEntryUtils.js b/ehr/resources/web/ehr/DataEntryUtils.js index d838a6473..5e926ea3b 100644 --- a/ehr/resources/web/ehr/DataEntryUtils.js +++ b/ehr/resources/web/ehr/DataEntryUtils.js @@ -908,9 +908,16 @@ EHR.DataEntryUtils = new function(){ calculateDrugVolume: function(valMap, rounding, fixedAmount){ var vol; if (!fixedAmount){ - // vol = dosage * weight / conc (ie. mg/kg * kg / mg/ml) if (valMap.concentration && valMap.dosage && valMap.weight){ - vol = valMap.dosage * valMap.weight / valMap.concentration; + if (valMap.dosage_units === 'ml/kg') { + // Some drugs are in ml/kg instead of mg/kg. In those cases, concentration is irrelevant. + vol = valMap.dosage * valMap.weight; + + } + else { + // vol = dosage * weight / conc (ie. mg/kg * kg / mg/ml) + vol = valMap.dosage * valMap.weight / valMap.concentration; + } } } else { diff --git a/ehr/resources/web/ehr/grid/Panel.js b/ehr/resources/web/ehr/grid/Panel.js index 0b43418f7..b1341ff56 100644 --- a/ehr/resources/web/ehr/grid/Panel.js +++ b/ehr/resources/web/ehr/grid/Panel.js @@ -20,6 +20,19 @@ Ext4.define('EHR.grid.Panel', { this.configureColumns(); this.sortColumns(); + var dockedItems = [{ + xtype: 'toolbar', + dock: 'top', + items: this.getTbarButtons() + }]; + if (this.formConfig.topAndBottomButtons) { + dockedItems.push({ + xtype: 'toolbar', + dock: 'bottom', + items: this.getTbarButtons() + }) + } + Ext4.apply(this, { cls: 'ldk-grid', clicksToEdit: 1, @@ -29,11 +42,7 @@ Ext4.define('EHR.grid.Panel', { defaults: { border: false }, - dockedItems: [{ - xtype: 'toolbar', - dock: 'top', - items: this.getTbarButtons() - }] + dockedItems: dockedItems }); if (this.allowDragDropReorder) { @@ -335,4 +344,4 @@ Ext4.define('EHR.grid.Panel', { return buttons; } -}); \ No newline at end of file +}); diff --git a/ehr/resources/web/ehr/model/sources/Default.js b/ehr/resources/web/ehr/model/sources/Default.js index 0e23bcfc3..12f89c3f8 100644 --- a/ehr/resources/web/ehr/model/sources/Default.js +++ b/ehr/resources/web/ehr/model/sources/Default.js @@ -655,6 +655,24 @@ EHR.model.DataModelManager.registerMetadata('Default', { columnConfig: { width: 160 } + }, + QCState: { + getInitialValue: function(v){ + var qc; + if (!v && EHR.Security.getQCStateByLabel('Completed')) + qc = EHR.Security.getQCStateByLabel('Completed').RowId; + return v || qc; + } + } + }, + 'study.geneticAncestry': { + QCState: { + getInitialValue: function(v){ + var qc; + if (!v && EHR.Security.getQCStateByLabel('Completed')) + qc = EHR.Security.getQCStateByLabel('Completed').RowId; + return v || qc; + } } }, 'study.Demographics': { diff --git a/ehr/resources/web/ehr/panel/AnimalGroupDetailsPanel.js b/ehr/resources/web/ehr/panel/AnimalGroupDetailsPanel.js index aad62e9d0..100bf018c 100644 --- a/ehr/resources/web/ehr/panel/AnimalGroupDetailsPanel.js +++ b/ehr/resources/web/ehr/panel/AnimalGroupDetailsPanel.js @@ -70,7 +70,7 @@ Ext4.define('EHR.panel.AnimalGroupDetailsPanel', { value: this.groupRow.getDisplayValue('purpose') },{ fieldLabel: 'Comments', - value: this.groupRow.getDisplayValue('comments') + value: this.groupRow.getDisplayValue('comment') }] }] }); diff --git a/ehr/resources/web/ehr/panel/ClinicalManagementPanel.js b/ehr/resources/web/ehr/panel/ClinicalManagementPanel.js index 881c718be..e2f5d03b5 100644 --- a/ehr/resources/web/ehr/panel/ClinicalManagementPanel.js +++ b/ehr/resources/web/ehr/panel/ClinicalManagementPanel.js @@ -270,7 +270,8 @@ Ext4.define('EHR.panel.ClinicalManagementPanel', { menu.floating = true; var owner = Ext4.create('Ext.panel.Panel', { - border: false + border: false, + width: 0 }); owner.render(el); menu.setFloatParent(owner); diff --git a/ehr/resources/web/ehr/utils.js b/ehr/resources/web/ehr/utils.js index e50ac56d8..24227b8af 100644 --- a/ehr/resources/web/ehr/utils.js +++ b/ehr/resources/web/ehr/utils.js @@ -529,8 +529,8 @@ EHR.Utils = new function(){ } //append non-removeable filters - if (LABKEY.DataRegions[dataRegionName].getBaseFilters().length){ - var array = LABKEY.DataRegions[dataRegionName].getBaseFilters(); + if (LABKEY.DataRegions[dataRegionName].filters && LABKEY.DataRegions[dataRegionName].filters){ + var array = LABKEY.DataRegions[dataRegionName].filters; for (var i=0;i _dataSources = new ArrayList<>(); + private List _dataSources = new ArrayList<>(); + private Logger _log = Logger.getLogger(ClinicalHistoryManager.class); - private ClinicalHistoryManager(){} + private ClinicalHistoryManager() + { + } public static ClinicalHistoryManager get() { @@ -72,7 +75,7 @@ public List getHistory(Container c, User u, String subjectId, Date m public Set getTypes(Container c, User u) { - Set types = new HashSet(); + Set types = new HashSet<>(); for (HistoryDataSource ds : getDataSources(c, u)) { @@ -100,7 +103,14 @@ public List getHistory(Container c, User u, String subjectId, String public void sortRowsByDate(List rows) { - rows.sort(Comparator.comparing(HistoryRow::getSortDateString, Comparator.reverseOrder())); + Collections.sort(rows, new Comparator() + { + @Override + public int compare(HistoryRow o1, HistoryRow o2) + { + return (-1 * (o1.getSortDateString().compareTo(o2.getSortDateString()))); + } + }); } protected List getDataSources(Container c, User u) diff --git a/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java b/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java index 2eb50cf81..bf19f1201 100644 --- a/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java +++ b/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java @@ -63,14 +63,15 @@ protected String getHtml(Container c, Results rs, boolean redacted) throws SQLEx { StringBuilder sb = new StringBuilder(); - if (!redacted) + if (!redacted && LabworkManager.get().showPerformedBy(c, rs.hasColumn(FieldKey.fromString("type")) ? rs.getString("type") : null)) + { sb.append(safeAppend(rs, "Performed By", "performedby")); + //Modified 10-13-2017 Blasa + sb.append(safeAppend(rs, "Testing Performed by", "createdby/DisplayName")); + } - //sb.append(safeAppend(rs, "Type", "type")); sb.append(safeAppend(rs, "Service/Panel", "servicerequested")); - //Modified 9-9-2015 Blasa - sb.append(safeAppend(rs, "Testing Performed by", "chargetype")); sb.append(safeAppend(rs, "Sample Type", "sampletype")); @@ -109,9 +110,8 @@ protected String getHtml(Container c, Results rs, boolean redacted) throws SQLEx @Override protected Set getColumnNames() { - //return PageFlowUtil.set("Id", "date", "enddate", "objectid", "type", "performedby", "sampletype", "tissue/meaning", "tissue", "collectionmethod", "method", "servicerequested", "remark"); - //Modified 9-9-2015 Added chargetype - return PageFlowUtil.set("Id", "date", "enddate", "objectid", "type", "performedby", "sampletype", "tissue/meaning", "tissue", "collectionmethod", "method", "servicerequested", "chargetype","remark"); + //Modified: 5-17-2017 R.Blasa + return PageFlowUtil.set("Id", "date", "enddate", "objectid", "type", "performedby", "sampletype", "tissue/meaning", "tissue", "collectionmethod", "method", "servicerequested", "createdby/DisplayName","remark"); } @Override diff --git a/ehr/src/org/labkey/ehr/history/LabworkManager.java b/ehr/src/org/labkey/ehr/history/LabworkManager.java index 1669c2f93..d87648306 100644 --- a/ehr/src/org/labkey/ehr/history/LabworkManager.java +++ b/ehr/src/org/labkey/ehr/history/LabworkManager.java @@ -15,6 +15,7 @@ */ package org.labkey.ehr.history; +import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.ehr.history.LabworkType; import org.labkey.api.security.User; @@ -110,4 +111,16 @@ private void merge(Map> map, Map> newM map.put(runId, existing); } } + + public boolean showPerformedBy(Container c, @Nullable String type) + { + for (LabworkType labworkType : _types) + { + if (labworkType.isEnabled(c) && labworkType.getName().equalsIgnoreCase(type)) + { + return labworkType.showPerformedBy(); + } + } + return true; + } } diff --git a/ehr/src/org/labkey/ehr/security/EHRProtocolManagementRole.java b/ehr/src/org/labkey/ehr/security/EHRProtocolManagementRole.java index e38cdf1f1..a87469312 100644 --- a/ehr/src/org/labkey/ehr/security/EHRProtocolManagementRole.java +++ b/ehr/src/org/labkey/ehr/security/EHRProtocolManagementRole.java @@ -27,6 +27,7 @@ * User: bimber * Date: 1/17/13 * Time: 7:42 PM +* 3/31/2017 jonesga removed ProjectEDit Permissions /// approved by j Eckels 3/30/2017 */ public class EHRProtocolManagementRole extends AbstractEHRRole { @@ -38,7 +39,7 @@ public EHRProtocolManagementRole() UpdatePermission.class, DeletePermission.class, EHRDataEntryPermission.class, - EHRProjectEditPermission.class, + EHRProtocolEditPermission.class ); } diff --git a/ehr/src/org/labkey/ehr/table/AbstractAgeDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AbstractAgeDisplayColumn.java new file mode 100644 index 000000000..0df82846c --- /dev/null +++ b/ehr/src/org/labkey/ehr/table/AbstractAgeDisplayColumn.java @@ -0,0 +1,13 @@ +package org.labkey.ehr.table; + +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.ehr.table.DurationColumn; + +public abstract class AbstractAgeDisplayColumn extends DurationColumn +{ + public AbstractAgeDisplayColumn(ColumnInfo col) + { + super(col, "birth", "lastDayAtCenter"); + setDropTime(true); + } +} diff --git a/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java index 7c6d965f4..42243c3b1 100644 --- a/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java @@ -16,8 +16,8 @@ package org.labkey.ehr.table; import org.apache.commons.lang3.time.DurationFormatUtils; +import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; -import org.labkey.api.ehr.table.DurationColumn; import java.util.Calendar; import java.util.Date; @@ -27,7 +27,7 @@ * Date: 10/23/13 * Time: 3:49 PM */ -public class AgeDisplayColumn extends DurationColumn +public class AgeDisplayColumn extends AbstractAgeDisplayColumn { public AgeDisplayColumn(ColumnInfo col) { @@ -35,17 +35,8 @@ public AgeDisplayColumn(ColumnInfo col) } @Override - public String getFormattedDuration(Date startDate, Date endDate) + public String getFormattedDuration(@NotNull Calendar birthCal, @NotNull Calendar deathCal) { - if (startDate == null) - return null; - - Calendar birthCal = Calendar.getInstance(); - birthCal.setTime(startDate); - - Calendar deathCal = Calendar.getInstance(); - deathCal.setTime(endDate == null ? new Date() : endDate); - String yearMonthPartFromUtil; String yearDayPartFromUtil; try diff --git a/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java index f9e109124..90e4f9fbf 100644 --- a/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java @@ -16,8 +16,8 @@ package org.labkey.ehr.table; import org.apache.commons.lang3.time.DurationFormatUtils; +import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; -import org.labkey.api.ehr.table.DurationColumn; import java.util.Calendar; import java.util.Date; @@ -27,7 +27,7 @@ * Date: 10/23/13 * Time: 3:49 PM */ -public class AgeMonthsDisplayColumn extends DurationColumn +public class AgeMonthsDisplayColumn extends AbstractAgeDisplayColumn { public AgeMonthsDisplayColumn(ColumnInfo col) { @@ -35,21 +35,12 @@ public AgeMonthsDisplayColumn(ColumnInfo col) } @Override - protected String getFormattedDuration(Date startDate, Date endDate) + protected String getFormattedDuration(@NotNull Calendar startDate, @NotNull Calendar endDate) { - if (startDate == null) - return null; - - Calendar birthCal = Calendar.getInstance(); - birthCal.setTime(startDate); - - Calendar deathCal = Calendar.getInstance(); - deathCal.setTime(endDate == null ? new Date() : endDate); - String monthDayPartFromUtil; try { - monthDayPartFromUtil = DurationFormatUtils.formatPeriod(birthCal.getTimeInMillis(), deathCal.getTimeInMillis(), "M:d"); + monthDayPartFromUtil = DurationFormatUtils.formatPeriod(startDate.getTimeInMillis(), endDate.getTimeInMillis(), "M:d"); } catch (IllegalArgumentException iae) { diff --git a/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java index 058f7587b..0a5ddee37 100644 --- a/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java @@ -16,13 +16,13 @@ package org.labkey.ehr.table; import org.apache.commons.lang3.time.DurationFormatUtils; +import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; -import org.labkey.api.ehr.table.DurationColumn; import java.util.Calendar; import java.util.Date; -public class AgeYearMonthsDisplayColumn extends DurationColumn +public class AgeYearMonthsDisplayColumn extends AbstractAgeDisplayColumn { public AgeYearMonthsDisplayColumn(ColumnInfo col) { @@ -30,17 +30,8 @@ public AgeYearMonthsDisplayColumn(ColumnInfo col) } @Override - protected String getFormattedDuration(Date startDate, Date endDate) + protected String getFormattedDuration(@NotNull Calendar birthCal, @NotNull Calendar deathCal) { - if (startDate == null) - return null; - - Calendar birthCal = Calendar.getInstance(); - birthCal.setTime(startDate); - - Calendar deathCal = Calendar.getInstance(); - deathCal.setTime(endDate == null ? new Date() : endDate); - String yearMonthPartFromUtil; try { diff --git a/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java index 5e9184c17..77a998aa6 100644 --- a/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java @@ -16,13 +16,13 @@ package org.labkey.ehr.table; import org.apache.commons.lang3.time.DurationFormatUtils; +import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; -import org.labkey.api.ehr.table.DurationColumn; import java.util.Calendar; import java.util.Date; -public class AgeYearsMonthsDaysDisplayColumn extends DurationColumn +public class AgeYearsMonthsDaysDisplayColumn extends AbstractAgeDisplayColumn { public AgeYearsMonthsDaysDisplayColumn(ColumnInfo col) { @@ -30,17 +30,8 @@ public AgeYearsMonthsDaysDisplayColumn(ColumnInfo col) } @Override - protected String getFormattedDuration(Date startDate, Date endDate) + protected String getFormattedDuration(@NotNull Calendar birthCal, @NotNull Calendar deathCal) { - if (startDate == null) - return null; - - Calendar birthCal = Calendar.getInstance(); - birthCal.setTime(startDate); - - Calendar deathCal = Calendar.getInstance(); - deathCal.setTime(endDate == null ? new Date() : endDate); - String formattedAge; try { diff --git a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java index 60f9927d1..9b34b92f6 100644 --- a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java +++ b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java @@ -41,6 +41,7 @@ import org.labkey.api.ehr.buttons.EHRShowEditUIButton; import org.labkey.api.ehr.security.EHRDataAdminPermission; import org.labkey.api.exp.api.StorageProvisioner; +import org.labkey.api.exp.property.Domain; import org.labkey.api.gwt.client.AuditBehaviorType; import org.labkey.api.gwt.client.FacetingBehaviorType; import org.labkey.api.ldk.LDKService; @@ -454,7 +455,7 @@ private void customizeDataset(DatasetTable ds) if (matches(ti, "study", "Treatment Orders")) { - addIsActiveColWithTime(ti); + addIsActiveCol(ti, true, EHRService.EndingOption.endingBeforeNow); } } else if (matches(ti, "study", "Clinical Encounters") || matches(ti, "study", "Encounters")) @@ -479,7 +480,7 @@ else if (matches(ti, "study", "pathologyDiagnoses") || matches(ti, "study", "Pat } else if (matches(ti, "study", "housing")) { - addIsActiveColWithTime(ti); + addIsActiveCol(ti, true, EHRService.EndingOption.endingBeforeNow); } else if (matches(ti, "study", "blood") || matches(ti, "study", "Blood Draws")) { @@ -503,16 +504,20 @@ else if (matches(ti, "study", "problem") || matches(ti, "study", "problem list") } else if (matches(ti, "study", "flags") || matches(ti, "study", "Animal Record Flags")) { - addIsActiveCol(ti, false); + addIsActiveCol(ti, false, EHRService.EndingOption.activeAfterMidnightTonight); } else if (matches(ti, "study", "diet")) { addIsActiveCol(ti); } - else if (matches(ti, "study", "parentage")) + else if (matches(ti, "study", "geneticAncestry")) { addIsActiveCol(ti, false); } + else if (matches(ti, "study", "parentage")) + { + addIsActiveCol(ti, false, EHRService.EndingOption.activeAfterMidnightTonight); + } else if (matches(ti, "study", "demographics")) { customizeDemographics(ti); @@ -531,15 +536,11 @@ else if (matches(ti, "study", "arrival")) private void addIsActiveCol(AbstractTableInfo ti) { - addIsActiveCol(ti, true); + addIsActiveCol(ti, false, EHRService.EndingOption.activeAfterMidnightTonight, EHRService.EndingOption.allowSameDay); } - private void addIsActiveCol(AbstractTableInfo ti, boolean allowSameDay) - { - addIsActiveCol(ti, allowSameDay, false); - } - private void addIsActiveCol(AbstractTableInfo ti, boolean allowSameDay, boolean allowDateOfDeath) + private void addIsActiveCol(AbstractTableInfo ti, boolean includeExpired, EHRService.EndingOption... endOptions) { if (ti.getColumn("date") == null || ti.getColumn("enddate") == null) { @@ -638,6 +639,21 @@ private void customizeStudyData(AbstractTableInfo ti) customizeButtonBar(ti); } + private void expandRemarksColumn(final AbstractTableInfo ti) + { + Dataset dataset = ((DatasetTable) ti).getDataset(); + Domain domain = dataset.getDomain(); + + // Hack the metadata for the length of the remark column, which has + // been altered in the DB so that it doesn't match with the standard + // "remark" property. See ONPRC ticket 33848 and EHRManager.ensureDatasetPropertyDescriptors() + TableInfo realTable = StorageProvisioner.getSchemaTableInfo(domain); + ColumnInfo remarkCol = realTable.getColumn("remark"); + remarkCol.setLocked(false); + remarkCol.setScale(1000000); + remarkCol.setLocked(true); + } + private void customizeEncountersTable(final AbstractTableInfo ti) { appendEncountersCol(ti, "participants", "Participants", "encounter_participants_summary"); @@ -645,11 +661,14 @@ private void customizeEncountersTable(final AbstractTableInfo ti) appendEncountersCol(ti, "flags", "Flags", "encounter_flags_summary"); appendSNOMEDCol(ti); + + expandRemarksColumn(ti); } private void customizeGrossFindings(final AbstractTableInfo ti) { appendSNOMEDCol(ti); + expandRemarksColumn(ti); } private void customizeHistology(final AbstractTableInfo ti) @@ -1300,7 +1319,7 @@ private void customizeDrugsUnified(AbstractTableInfo ti) { doSharedCustomization(ti); addUnitColumns(ti); - addIsActiveColWithTime(ti); + addIsActiveCol(ti, true, EHRService.EndingOption.endingBeforeNow); } private void customizeTasks(AbstractTableInfo ti) diff --git a/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java b/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java index e36404d2d..20a9ab5ce 100644 --- a/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java +++ b/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java @@ -1576,14 +1576,40 @@ public void updateStatusField(List ids, Map> liveBirt // NOTE: this behavior around live births is an imperfect way to mesh WNPRC/ONPRC rules. ONPRC records records in the birth table, // including dead infants. all records in the WNPRC table are of live births. checking for the column 'birth_condition' column is a crude proxy for this TableInfo birthTable = getTableInfo("study", "birth"); + TableInfo arrivalTable = getTableInfo("study", "Arrival"); //note: allow draft records to count SimpleFilter deadBirthFilter = new SimpleFilter(FieldKey.fromString("birth_condition/alive"), false); deadBirthFilter.addCondition(FieldKey.fromString("birth_condition"), null, CompareType.NONBLANK); - Date lastDeadBirth = birthTable.getColumnNameSet().contains("birth_condition") ? findMostRecentDate(id, getMostRecentDate(id, birthTable, deadBirthFilter), null) : null; - Date lastLiveBirth = findMostRecentDate(id, getMostRecentDate(id, birthTable, (birthTable.getColumnNameSet().contains("birth_condition") ? new SimpleFilter(FieldKey.fromString("birth_condition/alive"), false, CompareType.NEQ_OR_NULL) : null)), liveBirths); + boolean hasBirthConditionCol = birthTable.getColumnNameSet().contains("birth_condition"); + boolean hasArrivalAcquiTypeCol = arrivalTable.getColumnNameSet().contains("acquisitionType"); + Date lastDeadBirth = hasBirthConditionCol ? findMostRecentDate(id, getMostRecentDate(id, birthTable, deadBirthFilter), null) : null; + Date lastLiveBirth = findMostRecentDate(id, getMostRecentDate(id, birthTable, (hasBirthConditionCol ? new SimpleFilter(FieldKey.fromString("birth_condition/alive"), false, CompareType.NEQ_OR_NULL) : null)), liveBirths); - String status = null; - if (lastDeath != null || lastDeadBirth != null) + String birthCondition = null; + String acquitype = null; + if (hasBirthConditionCol) + { + TableSelector ts = new TableSelector(birthTable, Collections.singleton("birth_condition"), new SimpleFilter(FieldKey.fromParts("Id"), id), null); + birthCondition = ts.getObject(String.class); + } + if (hasArrivalAcquiTypeCol) + { + FieldKey acquisitionFieldKey = FieldKey.fromParts("acquisitionType", "value"); + Map columns = QueryService.get().getColumns(arrivalTable, Collections.singleton(acquisitionFieldKey)); + ColumnInfo acquisitionColumn = columns.get(acquisitionFieldKey); + TableSelector ts = new TableSelector(arrivalTable, Collections.singleton(acquisitionColumn), new SimpleFilter(FieldKey.fromParts("Id"), id), null); + acquitype = ts.getObject(String.class); + } + String status; + if ("Fetus - Prenatal".equalsIgnoreCase(birthCondition) ) + { + status = "Fetus"; + } + else if ("Pending Arrival".equalsIgnoreCase(acquitype)) + { + status = "Pending"; + } + else if (lastDeath != null || lastDeadBirth != null) { status = "Dead"; } From da1c620ac4f9184fdca59832444fa0eb668c3a3f Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 6 Oct 2020 14:28:14 -0700 Subject: [PATCH 02/34] Merge from onprc19.1 r.63282 --- EHR_ComplianceDB/resources/views/publicPage.html | 8 +++++++- .../dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql | 1 + ehr/resources/schemas/ehr_lookups.xml | 3 +++ .../org/labkey/ehr/table/DefaultEHRCustomizer.java | 13 +++++++++++++ 4 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql diff --git a/EHR_ComplianceDB/resources/views/publicPage.html b/EHR_ComplianceDB/resources/views/publicPage.html index 2cd3b1402..92ff487de 100644 --- a/EHR_ComplianceDB/resources/views/publicPage.html +++ b/EHR_ComplianceDB/resources/views/publicPage.html @@ -19,7 +19,13 @@ xtype: 'ldk-linkbutton', text: '
  • View Employee List
    • ', href: LABKEY.ActionURL.buildURL('query', 'executeQuery', null, {schemaName: 'EmployeeData', 'query.queryName': 'Employees'}) - },{ + }, +// { +// xtype: 'ldk-linkbutton', +// text: '
  • View Respirator Protection Quarantine Report
    • ', +// href: LABKEY.ActionURL.buildURL('query', 'executeQuery', null, {schemaName: 'EmployeeData', 'query.queryName': 'RespiratorProtectionQuarantine'}) +// }, + { xtype: 'ldk-linkbutton', text: '
  • View Private Section (authorized users only)
    • ', href: LABKEY.ActionURL.buildURL('project', 'start', container), diff --git a/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql b/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql new file mode 100644 index 000000000..5396c7f35 --- /dev/null +++ b/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql @@ -0,0 +1 @@ +ALTER TABLE ehr_lookups.flag_categories ADD datedisabled DATETIME; \ No newline at end of file diff --git a/ehr/resources/schemas/ehr_lookups.xml b/ehr/resources/schemas/ehr_lookups.xml index daac2f84d..c97fc3f7f 100644 --- a/ehr/resources/schemas/ehr_lookups.xml +++ b/ehr/resources/schemas/ehr_lookups.xml @@ -2710,6 +2710,9 @@ entityid     + + Date Disabled + diff --git a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java index 9b34b92f6..3123d4034 100644 --- a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java +++ b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java @@ -1798,6 +1798,7 @@ public TableInfo getLookupTableInfo() " ROUND(CONVERT(age_in_months(d.birth, CAST(c." + dateColName + " as DATE)), DOUBLE) / 12, 1)\n" + "END AS float) as AgeAtTime,\n" + "\n" + + "CAST(\n" + "CASE\n" + "WHEN d.birth is null or c." + dateColName + " is null\n" + @@ -1818,6 +1819,18 @@ public TableInfo getLookupTableInfo() " floor(age(d.birth, CAST(c." + dateColName + " as DATE)))\n" + "END AS float) as AgeAtTimeYearsRounded,\n" + "\n" + + //Added 'Age at time Days' by kollil on 02/15/2019 + "CAST(\n" + + "CASE\n" + + "WHEN d.birth is null or c." + dateColName + " is null\n" + + " THEN null\n" + + "WHEN (d.lastDayAtCenter IS NOT NULL AND d.lastDayAtCenter < c." + dateColName + ") THEN\n" + + " CONVERT(TIMESTAMPDIFF('SQL_TSI_DAY',d.birth, d.lastDayAtCenter), INTEGER)\n" + + "ELSE\n" + + " CONVERT(TIMESTAMPDIFF('SQL_TSI_DAY',d.birth, CAST(c." + dateColName + " AS DATE)), INTEGER)\n" + + "END AS float) as AgeAtTimeDays,\n" + + "\n" + + // "CAST(\n" + "CASE\n" + "WHEN d.birth is null or c." + dateColName + " is null\n" + From 25faf26f34eff78467940d29c5bf3a04d822e819 Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 6 Oct 2020 14:51:55 -0700 Subject: [PATCH 03/34] Merge from onprc19.1 r.63282 --- ehr/resources/schemas/ehr_lookups.xml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/ehr/resources/schemas/ehr_lookups.xml b/ehr/resources/schemas/ehr_lookups.xml index c97fc3f7f..d446ed732 100644 --- a/ehr/resources/schemas/ehr_lookups.xml +++ b/ehr/resources/schemas/ehr_lookups.xml @@ -2757,6 +2757,9 @@ entityid + + Date Disabled +
    From a01dd026e5352b001745530c7fadd7b1bff18c84 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 7 Oct 2020 00:31:11 -0700 Subject: [PATCH 04/34] Merge from onprc19.1 r.63328 to 64381 --- .../postgresql/ehr_lookups-17.20-17.21.sql | 3 + .../dbscripts/sqlserver/ehr-17.21-17.30.sql | 40 +++++++++++ .../labkey/ehr/table/AgeDisplayColumn.java | 2 +- .../ehr/table/AgeMonthsDisplayColumn.java | 2 +- .../ehr/table/AgeYearMonthsDisplayColumn.java | 2 +- .../AgeYearsMonthsDaysDisplayColumn.java | 2 +- .../test/tests/onprc_ehr/ONPRC_EHRTest.java | 66 +++++++++++++++++++ 7 files changed, 113 insertions(+), 4 deletions(-) create mode 100644 ehr/resources/schemas/dbscripts/postgresql/ehr_lookups-17.20-17.21.sql create mode 100644 ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql diff --git a/ehr/resources/schemas/dbscripts/postgresql/ehr_lookups-17.20-17.21.sql b/ehr/resources/schemas/dbscripts/postgresql/ehr_lookups-17.20-17.21.sql new file mode 100644 index 000000000..33b98ced3 --- /dev/null +++ b/ehr/resources/schemas/dbscripts/postgresql/ehr_lookups-17.20-17.21.sql @@ -0,0 +1,3 @@ +/* File copied from EHR version upgrade to 17.21 in onprc17.2Prod branch */ + +ALTER TABLE ehr_lookups.flag_categories ADD COLUMN datedisabled TIMESTAMP; \ No newline at end of file diff --git a/ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql b/ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql new file mode 100644 index 000000000..e820e0f89 --- /dev/null +++ b/ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql @@ -0,0 +1,40 @@ +/* + * Copyright (c) 2017 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +/* Copy of file to deal with EHR version upgrade to 17.21 in onprc17.2Prod branch */ + +/* ehr-17.20-17.21.sql */ + +CREATE TABLE ehr.observation_types ( + rowid INT IDENTITY(1,1) NOT NULL, + value varchar(200), + category varchar(200), + editorconfig varchar(4000), + schemaname varchar(200), + queryname varchar(200), + valuecolumn varchar(200), + Created DATETIME, + CreatedBy USERID, + Modified DATETIME, + ModifiedBy USERID, + Container entityId NOT NULL, + + CONSTRAINT PK_EHR_OBSERVATION_TYPES PRIMARY KEY (rowid), + CONSTRAINT FK_EHR_OBSERVATION_TYPES_CONTAINER FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +GO + +CREATE INDEX EHR_OBSERVATION_TYPES_CONTAINER_INDEX ON ehr.observation_types (Container); +GO + +/* ehr-17.21-17.22.sql */ + +ALTER TABLE ehr.protocol ADD Lsid LsidType null; +ALTER TABLE ehr.project ADD Lsid LsidType null; + +/* ehr-17.22-17.23.sql */ + +ALTER TABLE ehr.reports ADD ReportStatus NVARCHAR(MAX); \ No newline at end of file diff --git a/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java index 42243c3b1..8044b7846 100644 --- a/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeDisplayColumn.java @@ -31,7 +31,7 @@ public class AgeDisplayColumn extends AbstractAgeDisplayColumn { public AgeDisplayColumn(ColumnInfo col) { - super(col, "birth", "lastDayAtCenter"); + super(col); } @Override diff --git a/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java index 90e4f9fbf..a57b836f7 100644 --- a/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeMonthsDisplayColumn.java @@ -31,7 +31,7 @@ public class AgeMonthsDisplayColumn extends AbstractAgeDisplayColumn { public AgeMonthsDisplayColumn(ColumnInfo col) { - super(col, "birth", "lastDayAtCenter"); + super(col); } @Override diff --git a/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java index 0a5ddee37..ed2b2039c 100644 --- a/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeYearMonthsDisplayColumn.java @@ -26,7 +26,7 @@ public class AgeYearMonthsDisplayColumn extends AbstractAgeDisplayColumn { public AgeYearMonthsDisplayColumn(ColumnInfo col) { - super(col, "birth", "lastDayAtCenter"); + super(col); } @Override diff --git a/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java b/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java index 77a998aa6..69b630810 100644 --- a/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java +++ b/ehr/src/org/labkey/ehr/table/AgeYearsMonthsDaysDisplayColumn.java @@ -26,7 +26,7 @@ public class AgeYearsMonthsDaysDisplayColumn extends AbstractAgeDisplayColumn { public AgeYearsMonthsDaysDisplayColumn(ColumnInfo col) { - super(col, "birth", "lastDayAtCenter"); + super(col); } @Override diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 417674bf7..60fc69a76 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -2229,6 +2229,72 @@ private void setNecropsYFormElement(String id, String value) assertEquals(value, getFormElement(loc)); } + @Test + public void testNecropsyRequestFlow() + { + String animalId = "12345"; + LocalDateTime now = LocalDateTime.now(); + String projectId = "640991"; + String type = "Necropsy"; + String chargeType = "1"; + String procedureid = "Necropsy Grade 2: Standard"; + DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd"); + String tissue = "AMNION (T-88300)"; + + log("Begin the test with entry data page"); + EnterDataPage enterData = EnterDataPage.beginAt(this, getContainerPath()); + enterData.waitAndClickAndWait(Locator.linkWithText("Necropsy Request")); + waitForElement(Locator.pageHeader("Necropsy Request")); + + log("Setting the Necropsy details"); + setNecropsYFormElement("Id", animalId); + setNecropsYFormElement("date", now.format(formatter)); + click(Locator.tagWithClassContaining("div","x4-trigger-index-1")); + _ext4Helper.selectComboBoxItem("Center Project:",Ext4Helper.TextMatchTechnique.CONTAINS,"Other"); + _ext4Helper.selectComboBoxItem("Project:",Ext4Helper.TextMatchTechnique.CONTAINS,projectId); + clickButton("Submit",0); + _ext4Helper.selectComboBoxItem("Type:", Ext4Helper.TextMatchTechnique.CONTAINS,type); + setNecropsYFormElement("chargetype", chargeType); + _ext4Helper.selectComboBoxItem("Procedure:", Ext4Helper.TextMatchTechnique.CONTAINS, procedureid); + + log("Entering values for Tissue Samples"); + Ext4GridRef grid = _helper.getExt4GridForFormSection("Tissue Samples"); + _helper.addRecordToGrid(grid); + int index = grid.getRowCount(); + grid.setGridCell(index, "Id", animalId); + grid.setGridCell(index, "date", now.format(formatter)); + grid.setGridCell(index, "tissue", tissue); + + log("Entering values for Organ Weights"); + grid = _helper.getExt4GridForFormSection("Organ Weights"); + _helper.addRecordToGrid(grid); + index = grid.getRowCount(); + grid.setGridCell(index, "Id", animalId); + grid.setGridCell(index, "date", now.format(formatter)); + grid.setGridCell(index, "tissue", tissue); + + log("Submit the request and approve"); + clickButton("Request & Approve", 0); + + waitForElement(Locator.linkWithText("Pending Requests")); + assertElementPresent(Locator.linkWithText("Pending Requests")); + click(Locator.linkWithText("Approved Requests")); + + log("Verifying the submitted Necropsy Request"); + DataRegionTable regionTable = new DataRegionTable("query", getDriver()); + assertEquals("There should be single approved necropsy request", 1, regionTable.getDataRowCount()); + + //code to add for the remaining flow + } + + private void setNecropsYFormElement(String id, String value) + { + Locator loc = Locator.name(id); + waitForElement(loc); + setFormElement(loc, value); + assertEquals(value, getFormElement(loc)); + } + @Override protected String getAnimalHistoryPath() { From 2ed17672bdbf218fe8a811db42aa2f11d51026a2 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 7 Oct 2020 00:42:16 -0700 Subject: [PATCH 05/34] Merge from onprc19.1 r.64647 --- .../api/ehr/history/DefaultLabworkType.java | 4 ++++ .../reports/schemas/study/Pedigree/Pedigree.r | 2 +- .../web/ehr/panel/HousingDataEntryPanel.js | 2 +- .../web/ehr/panel/ManageTreatmentsPanel.js | 9 +++++++++ .../labkey/ehr/utils/TriggerScriptHelper.java | 17 +++++++++++++++-- 5 files changed, 30 insertions(+), 4 deletions(-) diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java index e24718f24..af79e3021 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java @@ -230,6 +230,10 @@ protected String getLine(Results rs, boolean redacted) throws SQLException StringBuilder sb = new StringBuilder(); String testId = getTestId(rs); Double result = _resultField == null ? null : rs.getDouble(FieldKey.fromString(_resultField)); + if (rs.wasNull()) + { + result = null; + } String units = _unitsField == null ? null : rs.getString(FieldKey.fromString(_unitsField)); String qualResult = _qualResultField == null ? null : rs.getString(FieldKey.fromString(_qualResultField)); diff --git a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r index bda5bf9a1..f7d13cca4 100644 --- a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r +++ b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r @@ -13,7 +13,7 @@ library(Rlabkey) #str(labkey.data); #warnings(); -labkey.acceptSelfSignedCerts(); +labkey.setCurlOptions(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE) if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$sire))){ diff --git a/ehr/resources/web/ehr/panel/HousingDataEntryPanel.js b/ehr/resources/web/ehr/panel/HousingDataEntryPanel.js index d9c9a8eb2..9c848e11d 100644 --- a/ehr/resources/web/ehr/panel/HousingDataEntryPanel.js +++ b/ehr/resources/web/ehr/panel/HousingDataEntryPanel.js @@ -17,7 +17,7 @@ Ext4.define('EHR.panel.HousingDataEntryPanel', { LDK.Assert.assertNotEmpty('Unable to find housing store in HousingDataEntryPanel', store); if (extraContext && extraContext.successURL && store.getCount() > 0){ - Ext4.Msg.confirm('Success', 'Do you want to view to room layout now? This will allow you to verify and/or change dividers', function(val){ + Ext4.Msg.confirm('Success', 'Do you want to view the room layout now? This will allow you to verify and/or change dividers', function(val){ window.onbeforeunload = Ext4.emptyFn; if (val == 'yes'){ diff --git a/ehr/resources/web/ehr/panel/ManageTreatmentsPanel.js b/ehr/resources/web/ehr/panel/ManageTreatmentsPanel.js index f1b53e302..8e9e147c0 100644 --- a/ehr/resources/web/ehr/panel/ManageTreatmentsPanel.js +++ b/ehr/resources/web/ehr/panel/ManageTreatmentsPanel.js @@ -86,6 +86,15 @@ Ext4.define('EHR.panel.ManageTreatmentsPanel', { defaultValue: animalId, editable: false }, + //Added: 7-10-2019 R.Blasa + frequency: { + allowBlank: false, + lookup: { + sort: 'sort_order', + filterArray: [LABKEY.Filter.create('active', true, LABKEY.Filter.Types.EQUAL)], + columns: '*' + } + }, category: { defaultValue: category } diff --git a/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java b/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java index 20a9ab5ce..35bf8d485 100644 --- a/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java +++ b/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java @@ -367,8 +367,21 @@ public String validateAssignment(String id, Integer projectId, Date date) if (protocol == null) return "This project is not associated with a valid protocol"; - ProjectValidator validator = EHRService.get().getProjectValidator(); - return validator != null ? validator.validateAssignment(id, projectId, date, _user, getContainer(), protocol) : null; + TableInfo ti = getTableInfo("study", "Assignment"); + SimpleFilter filter = new SimpleFilter(FieldKey.fromString("Id"), id); + + filter.addCondition(FieldKey.fromString("date"), date, CompareType.DATE_LTE); + filter.addClause(new SimpleFilter.OrClause(new CompareType.EqualsCompareClause(FieldKey.fromString("project"), CompareType.EQUAL, projectId), new CompareType.CompareClause(FieldKey.fromString("project/protocol"), CompareType.EQUAL, protocol))); + filter.addClause(new SimpleFilter.OrClause(CompareType.DATE_GTE.createFilterClause(FieldKey.fromString("enddate"), date), new CompareType.CompareClause(FieldKey.fromString("enddate"), CompareType.ISBLANK, null))); + filter.addCondition(FieldKey.fromString("qcstate/publicdata"), true, CompareType.EQUAL); + + TableSelector ts = new TableSelector(ti, PageFlowUtil.set("project"), filter, null); + if (!ts.exists()) + { + return "Not assigned to the protocol on this date"; + } + + return null; } public String getAccountForProject(int projectId) From 7b2397547a64c1c647528f07c82751b20baf6d06 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 7 Oct 2020 15:38:26 -0700 Subject: [PATCH 06/34] Merge from onprc19.1 r.64648 --- .../a_ehr_lookups-17.20-17.21.sql} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename ehr/resources/schemas/dbscripts/{postgresql/ehr_lookups-17.20-17.21.sql => sqlserver/a_ehr_lookups-17.20-17.21.sql} (50%) diff --git a/ehr/resources/schemas/dbscripts/postgresql/ehr_lookups-17.20-17.21.sql b/ehr/resources/schemas/dbscripts/sqlserver/a_ehr_lookups-17.20-17.21.sql similarity index 50% rename from ehr/resources/schemas/dbscripts/postgresql/ehr_lookups-17.20-17.21.sql rename to ehr/resources/schemas/dbscripts/sqlserver/a_ehr_lookups-17.20-17.21.sql index 33b98ced3..a022a3ce9 100644 --- a/ehr/resources/schemas/dbscripts/postgresql/ehr_lookups-17.20-17.21.sql +++ b/ehr/resources/schemas/dbscripts/sqlserver/a_ehr_lookups-17.20-17.21.sql @@ -1,3 +1,3 @@ /* File copied from EHR version upgrade to 17.21 in onprc17.2Prod branch */ -ALTER TABLE ehr_lookups.flag_categories ADD COLUMN datedisabled TIMESTAMP; \ No newline at end of file +ALTER TABLE ehr_lookups.flag_categories ADD datedisabled DATETIME; \ No newline at end of file From 50b0d32c5a3b6598abcf67ce75865881d1b7b50d Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 7 Oct 2020 15:48:58 -0700 Subject: [PATCH 07/34] Merge from onprc19.1 r.64649 to 64652 --- .../schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql b/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql index 5396c7f35..a022a3ce9 100644 --- a/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql +++ b/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql @@ -1 +1,3 @@ +/* File copied from EHR version upgrade to 17.21 in onprc17.2Prod branch */ + ALTER TABLE ehr_lookups.flag_categories ADD datedisabled DATETIME; \ No newline at end of file From 6d7ff622e9d5a33ee3ca745d6e81c6682214cd05 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 7 Oct 2020 16:44:04 -0700 Subject: [PATCH 08/34] Merge from onprc19.1 r.64748 --- .../dbscripts/sqlserver/EHR_ComplianceDB-12.39-12.40.sql | 2 ++ .../src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.39-12.40.sql diff --git a/EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.39-12.40.sql b/EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.39-12.40.sql new file mode 100644 index 000000000..088f94886 --- /dev/null +++ b/EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.39-12.40.sql @@ -0,0 +1,2 @@ +ALTER TABLE ehr_compliancedb.Employees ALTER COLUMN Notes NVARCHAR (4000); + diff --git a/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java b/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java index d3d390318..ed0734f0c 100644 --- a/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java +++ b/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java @@ -49,7 +49,7 @@ public String getName() @Override public @Nullable Double getSchemaVersion() { - return 12.39; + return 12.40; } @Override From 6b6e16f71529ca589b6dba3e65f102cb5aabf6f5 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 7 Oct 2020 19:36:41 -0700 Subject: [PATCH 09/34] Merge from onprc19.1 r.64953 to 65052 --- .../web/ehr/data/DataEntryServerStore.js | 22 +++++++++++++------ 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/ehr/resources/web/ehr/data/DataEntryServerStore.js b/ehr/resources/web/ehr/data/DataEntryServerStore.js index dd94b72c4..e77ed8242 100644 --- a/ehr/resources/web/ehr/data/DataEntryServerStore.js +++ b/ehr/resources/web/ehr/data/DataEntryServerStore.js @@ -552,16 +552,24 @@ Ext4.define('EHR.data.DataEntryServerStore', { //transfer values var clientVal = Ext4.isEmpty(clientModel.get(clientFieldName)) ? null : clientModel.get(clientFieldName); var serverVal = Ext4.isEmpty(serverModel.get(serverFieldName)) ? null : serverModel.get(serverFieldName); - if (serverVal != clientVal){ - changedData = true; + + // See if the server and client disagree on the values at this point + var needToSetModel = serverVal !== clientVal; + // The client may already match if its value happens to be set by getInitialValue() and + // we're loading an existing record. If so, we still may need to push it into the raw part + // of the record + var needToSetRawModel = clientModel.raw && (needToSetModel || !clientModel.raw[clientFieldName]); + + if (needToSetModel){ + changedData = true; clientModel.set(clientFieldName, serverVal); - if (serverModel.raw && serverModel.raw[serverFieldName]){ - clientModel.raw[clientFieldName] = clientModel.raw[clientFieldName] || {}; - Ext4.apply(clientModel.raw[clientFieldName], serverModel.raw[serverFieldName]); - delete clientModel.raw[clientFieldName].url; - } changedStoreIDs[clientStore.storeId] = true; } + if (needToSetRawModel && serverModel.raw && serverModel.raw[serverFieldName]){ + clientModel.raw[clientFieldName] = clientModel.raw[clientFieldName] || {}; + Ext4.apply(clientModel.raw[clientFieldName], serverModel.raw[serverFieldName]); + delete clientModel.raw[clientFieldName].url; + } } //also sync server errors From efbb2cfe81bf6221385f408e953bb67a62d0b4a9 Mon Sep 17 00:00:00 2001 From: Binal Date: Thu, 8 Oct 2020 00:20:26 -0700 Subject: [PATCH 10/34] Merge from onprc19.1 r.65678 to 65757 --- ehr/resources/queries/study/treatment_order.query.xml | 2 +- ehr/resources/web/ehr/form/field/SnomedCodesEditor.js | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ehr/resources/queries/study/treatment_order.query.xml b/ehr/resources/queries/study/treatment_order.query.xml index c2f6f03a3..d86da1218 100644 --- a/ehr/resources/queries/study/treatment_order.query.xml +++ b/ehr/resources/queries/study/treatment_order.query.xml @@ -60,7 +60,7 @@ Frequency ehr_lookups - treatment_frequency + Treatment_Frequencies_Active rowid diff --git a/ehr/resources/web/ehr/form/field/SnomedCodesEditor.js b/ehr/resources/web/ehr/form/field/SnomedCodesEditor.js index eb4561516..a5c336754 100644 --- a/ehr/resources/web/ehr/form/field/SnomedCodesEditor.js +++ b/ehr/resources/web/ehr/form/field/SnomedCodesEditor.js @@ -174,7 +174,7 @@ Ext4.define('EHR.window.SnomedCodeWindow', { items: [{ xtype: 'button', style: 'margin-right: 5px;', - width: 20, + width: 28, testLocator: 'snomedUpArrow', icon: LABKEY.ActionURL.getContextPath() + '/_images/uparrow.gif', //text: 'Up', @@ -195,7 +195,7 @@ Ext4.define('EHR.window.SnomedCodeWindow', { },{ xtype: 'button', style: 'margin-right: 5px;', - width: 20, + width: 28, testLocator: 'snomedDownArrow', icon: LABKEY.ActionURL.getContextPath() + '/_images/downarrow.gif', handler: function(btn){ @@ -215,7 +215,7 @@ Ext4.define('EHR.window.SnomedCodeWindow', { },{ xtype: 'button', style: 'margin-right: 5px;', - width: 20, + width: 28, testLocator: 'snomedDelete', icon: LABKEY.ActionURL.getContextPath() + '/_images/delete.gif', handler: function(btn){ From 4a03e01c6e5ff0060fc9fca8e15c06775766de3a Mon Sep 17 00:00:00 2001 From: Binal Date: Sat, 10 Oct 2020 12:12:08 -0700 Subject: [PATCH 11/34] Fix build issues --- ehr/src/org/labkey/ehr/EHRServiceImpl.java | 49 +++++++++++++++++++ .../ehr/table/DefaultEHRCustomizer.java | 28 +---------- 2 files changed, 51 insertions(+), 26 deletions(-) diff --git a/ehr/src/org/labkey/ehr/EHRServiceImpl.java b/ehr/src/org/labkey/ehr/EHRServiceImpl.java index e38bfc625..8154cc3e7 100644 --- a/ehr/src/org/labkey/ehr/EHRServiceImpl.java +++ b/ehr/src/org/labkey/ehr/EHRServiceImpl.java @@ -679,6 +679,55 @@ public boolean hasPermission (String schemaName, String queryName, Container c, return EHRSecurityManager.get().testPermission(u, sr, perm, qcState); } + @Override + public void addIsActiveCol(AbstractTableInfo ti, boolean includeExpired, EndingOption... endOptions) + { + if (ti.getColumn("date") == null || ti.getColumn("enddate") == null) + { + return; + } + + String name = "isActive"; + if (ti.getColumn(name) == null) + { + SQLFragment sql = new SQLFragment("(CASE " + + // when the start is in the future, using whole-day increments, it is not active + " WHEN (CAST(" + ExprColumn.STR_TABLE_ALIAS + ".date as DATE) > {fn curdate()}) THEN " + ti.getSqlDialect().getBooleanFALSE() + + // when enddate is null, it is active + " WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NULL) THEN " + ti.getSqlDialect().getBooleanTRUE()); + for (EHRService.EndingOption endOption : endOptions) + { + sql.append(endOption.getSql()); + } + sql.append( + " WHEN (CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) > {fn curdate()}) THEN " + ti.getSqlDialect().getBooleanTRUE() + + " ELSE " + ti.getSqlDialect().getBooleanFALSE() + + " END)"); + + ExprColumn col = new ExprColumn(ti, name, sql, JdbcType.BOOLEAN, ti.getColumn("date"), ti.getColumn("enddate")); + col.setLabel("Is Active?"); + ti.addColumn(col); + } + + if (includeExpired) + { + String expired = "isExpired"; + if (ti.getColumn(expired) == null) + { + SQLFragment sql = new SQLFragment("(CASE " + + // any record with a null or future enddate (considering time) is active + " WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NULL) THEN " + ti.getSqlDialect().getBooleanFALSE() + + " WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate < {fn now()}) THEN " + ti.getSqlDialect().getBooleanTRUE() + + " ELSE " + ti.getSqlDialect().getBooleanFALSE() + + " END)"); + + ExprColumn col = new ExprColumn(ti, expired, sql, JdbcType.BOOLEAN, ti.getColumn("enddate")); + col.setLabel("Is Expired?"); + ti.addColumn(col); + } + } + } + @Override public void customizeDateColumn(AbstractTableInfo ti, String colName) { diff --git a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java index 3123d4034..da92c0f11 100644 --- a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java +++ b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java @@ -542,31 +542,7 @@ private void addIsActiveCol(AbstractTableInfo ti) private void addIsActiveCol(AbstractTableInfo ti, boolean includeExpired, EHRService.EndingOption... endOptions) { - if (ti.getColumn("date") == null || ti.getColumn("enddate") == null) - { - return; - } - - String name = "isActive"; - if (ti.getColumn(name, false) == null) - { - SQLFragment sql = new SQLFragment("(CASE " + - // when the start is in the future, using whole-day increments, it is not active - " WHEN (CAST(" + ExprColumn.STR_TABLE_ALIAS + ".date as DATE) > {fn curdate()}) THEN " + ti.getSqlDialect().getBooleanFALSE() + - // when enddate is null, it is active - " WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NULL) THEN " + ti.getSqlDialect().getBooleanTRUE() + - // if allowSameDay=true, then consider records that start/stop on today's date to be active - (allowSameDay ? " WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NOT NULL AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) = {fn curdate()} AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".date as DATE) = {fn curdate()}) THEN " + ti.getSqlDialect().getBooleanTRUE() : "") + - // if enddate is in the future (whole-day increments), then it is active - " WHEN (CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) > {fn curdate()}) THEN " + ti.getSqlDialect().getBooleanTRUE() + - //(allowDateOfDeath ? " WHEN " + ExprColumn.STR_TABLE_ALIAS : "") + - " ELSE " + ti.getSqlDialect().getBooleanFALSE() + - " END)"); - - ExprColumn col = new ExprColumn(ti, name, sql, JdbcType.BOOLEAN, ti.getColumn("date"), ti.getColumn("enddate")); - col.setLabel("Is Active?"); - ti.addColumn(col); - } + EHRService.get().addIsActiveCol(ti, includeExpired, endOptions); } //note: intended specially for treatment orders, but also used for housing. note slightly unusual behavior around start date @@ -648,7 +624,7 @@ private void expandRemarksColumn(final AbstractTableInfo ti) // been altered in the DB so that it doesn't match with the standard // "remark" property. See ONPRC ticket 33848 and EHRManager.ensureDatasetPropertyDescriptors() TableInfo realTable = StorageProvisioner.getSchemaTableInfo(domain); - ColumnInfo remarkCol = realTable.getColumn("remark"); + MutableColumnInfo remarkCol = (MutableColumnInfo) realTable.getColumn("remark"); remarkCol.setLocked(false); remarkCol.setScale(1000000); remarkCol.setLocked(true); From 8b7452f9550db4a9b437cf3704dd9a98eb0d0d1b Mon Sep 17 00:00:00 2001 From: Binal Date: Sat, 10 Oct 2020 12:40:49 -0700 Subject: [PATCH 12/34] Merge from onprc19.1Prod r 65762 to 65949 --- .../resources/schemas/ehr_compliancedb.xml | 3 --- .../reports/schemas/study/Pedigree/Pedigree.r | 10 +++++----- ehr/resources/web/ehr/panel/BulkEditPanel.js | 1 + ehr/resources/web/ehr/plugin/RowEditor.js | 2 +- ehr/resources/web/ehr/window/BulkEditWindow.js | 2 +- ehr/src/org/labkey/ehr/EHRController.java | 2 +- 6 files changed, 9 insertions(+), 11 deletions(-) diff --git a/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml b/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml index 6549d3634..a2f83fe82 100644 --- a/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml +++ b/EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml @@ -93,18 +93,15 @@ Last Name - 100 ALWAYS_OFF true First Name - 100 ALWAYS_OFF Middle Name - 100 ALWAYS_OFF diff --git a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r index f7d13cca4..e4d260099 100644 --- a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r +++ b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r @@ -16,7 +16,7 @@ library(Rlabkey) labkey.setCurlOptions(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE) -if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$sire))){ +if ((length(labkey.data$id) == 0) || (is.na(labkey.data$dam) & is.na(labkey.data$sire))){ png(filename="${imgout:myscatterplot}", width = 650, height = 150); plot(0, 0, type='n', xaxt='n', yaxt='n', bty='n', ann=FALSE ) title(main = "No pedigree data found for selected animal(s).", sub = NULL, xlab = NULL, ylab = NULL, @@ -200,8 +200,8 @@ if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$ if (length(damIndex) == 0) damIndex <- which(allPed$Id == ped$Dam[i]); if (length(sireIndex) == 0) sireIndex <- which(allPed$Id == ped$Sire[i]); - if((is.na(ped$Sire[i]))& (!is.na(ped$Dam[i]))){ - xt <- sample (1:30,1) + if(is.na(ped$Sire[i])){ + xt <- sample (1:99,1) #typeof(ped$Sire); #typeof(xt); ped$Sire[i] <- paste('xxs',xt) @@ -209,8 +209,8 @@ if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$ #print(ped$Dam[i]) #print(ped$Sire[i]) } - if((is.na(ped$Dam[i]))& (!is.na(ped$Sire[i]))){ - xt <- sample (1:30,1) + if(is.na(ped$Dam[i])){ + xt <- sample (1:99,1) #typeof(ped$Sire); #typeof(xt); ped$Dam[i] <- paste ('xxd',xt); diff --git a/ehr/resources/web/ehr/panel/BulkEditPanel.js b/ehr/resources/web/ehr/panel/BulkEditPanel.js index 03dc074d8..bb3af96a4 100644 --- a/ehr/resources/web/ehr/panel/BulkEditPanel.js +++ b/ehr/resources/web/ehr/panel/BulkEditPanel.js @@ -38,6 +38,7 @@ Ext4.define('EHR.panel.BulkEditPanel', { formConfig: this.formConfig, store: this.getStoreCopy(), textareaFieldWidth: EHR.form.Panel.defaultFieldWidth, + maxFieldWidth: EHR.form.Panel.defaultFieldWidth, bindConfig: { createRecordOnLoad: true } diff --git a/ehr/resources/web/ehr/plugin/RowEditor.js b/ehr/resources/web/ehr/plugin/RowEditor.js index d8977d5a2..6e3eccc21 100644 --- a/ehr/resources/web/ehr/plugin/RowEditor.js +++ b/ehr/resources/web/ehr/plugin/RowEditor.js @@ -104,7 +104,7 @@ Ext4.define('EHR.plugin.RowEditor', { if (cols > 1){ var newWidth = cols * (EHR.form.Panel.defaultFieldWidth + 20); if (newWidth > win.width) { - win.setWidth(); + win.setWidth(newWidth); } } }, diff --git a/ehr/resources/web/ehr/window/BulkEditWindow.js b/ehr/resources/web/ehr/window/BulkEditWindow.js index 48f48dde4..72eea0449 100644 --- a/ehr/resources/web/ehr/window/BulkEditWindow.js +++ b/ehr/resources/web/ehr/window/BulkEditWindow.js @@ -30,7 +30,7 @@ Ext4.define('EHR.window.BulkEditWindow', { beforerender: function(win){ var cols = win.down('#formPanel').items.get(0).items.getCount(); if (cols > 1){ - win.setWidth(cols * (EHR.form.Panel.defaultFieldWidth + 20)); + win.setWidth(cols * (EHR.form.Panel.defaultFieldWidth + 30)); } } } diff --git a/ehr/src/org/labkey/ehr/EHRController.java b/ehr/src/org/labkey/ehr/EHRController.java index 22a49b5fd..3d537fb5d 100644 --- a/ehr/src/org/labkey/ehr/EHRController.java +++ b/ehr/src/org/labkey/ehr/EHRController.java @@ -1447,7 +1447,7 @@ public ModelAndView getView(EnterDataForm form, BindException errors) } _title = _def.getLabel(); - + getPageConfig().setIncludePostParameters(true); return _def.createView(); } From 95fe82dad1fa20221ed432e196c8b343f2de281e Mon Sep 17 00:00:00 2001 From: Binal Date: Sun, 11 Oct 2020 10:37:35 -0700 Subject: [PATCH 13/34] Remove code duplication from the merge. --- .../test/tests/onprc_ehr/ONPRC_EHRTest.java | 66 ------------------- 1 file changed, 66 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 60fc69a76..417674bf7 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -2229,72 +2229,6 @@ private void setNecropsYFormElement(String id, String value) assertEquals(value, getFormElement(loc)); } - @Test - public void testNecropsyRequestFlow() - { - String animalId = "12345"; - LocalDateTime now = LocalDateTime.now(); - String projectId = "640991"; - String type = "Necropsy"; - String chargeType = "1"; - String procedureid = "Necropsy Grade 2: Standard"; - DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd"); - String tissue = "AMNION (T-88300)"; - - log("Begin the test with entry data page"); - EnterDataPage enterData = EnterDataPage.beginAt(this, getContainerPath()); - enterData.waitAndClickAndWait(Locator.linkWithText("Necropsy Request")); - waitForElement(Locator.pageHeader("Necropsy Request")); - - log("Setting the Necropsy details"); - setNecropsYFormElement("Id", animalId); - setNecropsYFormElement("date", now.format(formatter)); - click(Locator.tagWithClassContaining("div","x4-trigger-index-1")); - _ext4Helper.selectComboBoxItem("Center Project:",Ext4Helper.TextMatchTechnique.CONTAINS,"Other"); - _ext4Helper.selectComboBoxItem("Project:",Ext4Helper.TextMatchTechnique.CONTAINS,projectId); - clickButton("Submit",0); - _ext4Helper.selectComboBoxItem("Type:", Ext4Helper.TextMatchTechnique.CONTAINS,type); - setNecropsYFormElement("chargetype", chargeType); - _ext4Helper.selectComboBoxItem("Procedure:", Ext4Helper.TextMatchTechnique.CONTAINS, procedureid); - - log("Entering values for Tissue Samples"); - Ext4GridRef grid = _helper.getExt4GridForFormSection("Tissue Samples"); - _helper.addRecordToGrid(grid); - int index = grid.getRowCount(); - grid.setGridCell(index, "Id", animalId); - grid.setGridCell(index, "date", now.format(formatter)); - grid.setGridCell(index, "tissue", tissue); - - log("Entering values for Organ Weights"); - grid = _helper.getExt4GridForFormSection("Organ Weights"); - _helper.addRecordToGrid(grid); - index = grid.getRowCount(); - grid.setGridCell(index, "Id", animalId); - grid.setGridCell(index, "date", now.format(formatter)); - grid.setGridCell(index, "tissue", tissue); - - log("Submit the request and approve"); - clickButton("Request & Approve", 0); - - waitForElement(Locator.linkWithText("Pending Requests")); - assertElementPresent(Locator.linkWithText("Pending Requests")); - click(Locator.linkWithText("Approved Requests")); - - log("Verifying the submitted Necropsy Request"); - DataRegionTable regionTable = new DataRegionTable("query", getDriver()); - assertEquals("There should be single approved necropsy request", 1, regionTable.getDataRowCount()); - - //code to add for the remaining flow - } - - private void setNecropsYFormElement(String id, String value) - { - Locator loc = Locator.name(id); - waitForElement(loc); - setFormElement(loc, value); - assertEquals(value, getFormElement(loc)); - } - @Override protected String getAnimalHistoryPath() { From 3472a0e1f3e9f137476c44346d8b9ce71af29a24 Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 13 Oct 2020 09:53:14 -0700 Subject: [PATCH 14/34] 'datedisabled' listed twice - remove duplicate --- ehr/resources/schemas/ehr_lookups.xml | 3 --- 1 file changed, 3 deletions(-) diff --git a/ehr/resources/schemas/ehr_lookups.xml b/ehr/resources/schemas/ehr_lookups.xml index d446ed732..f6f52f143 100644 --- a/ehr/resources/schemas/ehr_lookups.xml +++ b/ehr/resources/schemas/ehr_lookups.xml @@ -2710,9 +2710,6 @@ entityid - - Date Disabled -
    From d63db3c89d2a71b18a7f79b558d51970a561b3d8 Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 13 Oct 2020 10:35:26 -0700 Subject: [PATCH 15/34] Remove 17.x scripts (content already part of rolled up scripts). Minor updates to metadata. --- .../sqlserver/EHR_Lookups-17.20-17.21.sql | 3 -- .../sqlserver/a_ehr_lookups-17.20-17.21.sql | 3 -- .../dbscripts/sqlserver/ehr-17.21-17.30.sql | 40 ------------------- ehr/resources/schemas/ehr_lookups.xml | 7 ++-- 4 files changed, 3 insertions(+), 50 deletions(-) delete mode 100644 ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql delete mode 100644 ehr/resources/schemas/dbscripts/sqlserver/a_ehr_lookups-17.20-17.21.sql delete mode 100644 ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql diff --git a/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql b/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql deleted file mode 100644 index a022a3ce9..000000000 --- a/ehr/resources/schemas/dbscripts/sqlserver/EHR_Lookups-17.20-17.21.sql +++ /dev/null @@ -1,3 +0,0 @@ -/* File copied from EHR version upgrade to 17.21 in onprc17.2Prod branch */ - -ALTER TABLE ehr_lookups.flag_categories ADD datedisabled DATETIME; \ No newline at end of file diff --git a/ehr/resources/schemas/dbscripts/sqlserver/a_ehr_lookups-17.20-17.21.sql b/ehr/resources/schemas/dbscripts/sqlserver/a_ehr_lookups-17.20-17.21.sql deleted file mode 100644 index a022a3ce9..000000000 --- a/ehr/resources/schemas/dbscripts/sqlserver/a_ehr_lookups-17.20-17.21.sql +++ /dev/null @@ -1,3 +0,0 @@ -/* File copied from EHR version upgrade to 17.21 in onprc17.2Prod branch */ - -ALTER TABLE ehr_lookups.flag_categories ADD datedisabled DATETIME; \ No newline at end of file diff --git a/ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql b/ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql deleted file mode 100644 index e820e0f89..000000000 --- a/ehr/resources/schemas/dbscripts/sqlserver/ehr-17.21-17.30.sql +++ /dev/null @@ -1,40 +0,0 @@ -/* - * Copyright (c) 2017 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 - */ - -/* Copy of file to deal with EHR version upgrade to 17.21 in onprc17.2Prod branch */ - -/* ehr-17.20-17.21.sql */ - -CREATE TABLE ehr.observation_types ( - rowid INT IDENTITY(1,1) NOT NULL, - value varchar(200), - category varchar(200), - editorconfig varchar(4000), - schemaname varchar(200), - queryname varchar(200), - valuecolumn varchar(200), - Created DATETIME, - CreatedBy USERID, - Modified DATETIME, - ModifiedBy USERID, - Container entityId NOT NULL, - - CONSTRAINT PK_EHR_OBSERVATION_TYPES PRIMARY KEY (rowid), - CONSTRAINT FK_EHR_OBSERVATION_TYPES_CONTAINER FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) -); -GO - -CREATE INDEX EHR_OBSERVATION_TYPES_CONTAINER_INDEX ON ehr.observation_types (Container); -GO - -/* ehr-17.21-17.22.sql */ - -ALTER TABLE ehr.protocol ADD Lsid LsidType null; -ALTER TABLE ehr.project ADD Lsid LsidType null; - -/* ehr-17.22-17.23.sql */ - -ALTER TABLE ehr.reports ADD ReportStatus NVARCHAR(MAX); \ No newline at end of file diff --git a/ehr/resources/schemas/ehr_lookups.xml b/ehr/resources/schemas/ehr_lookups.xml index f6f52f143..a4cfb2288 100644 --- a/ehr/resources/schemas/ehr_lookups.xml +++ b/ehr/resources/schemas/ehr_lookups.xml @@ -2637,7 +2637,9 @@ entityid - + + Date Disabled +
    @@ -2754,9 +2756,6 @@ entityid - - Date Disabled -
    From 23c1f481aea60ce02ffc2cbf53b96cc6f65622d5 Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 13 Oct 2020 17:07:58 -0700 Subject: [PATCH 16/34] Code review changes: - Add matching postgres script for EHR_ComplianceDB-12.39-12.40.sql - Add Treatment_Frequencies_Active.sql - Other minor cleanup --- .../dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql | 1 + .../queries/ehr_lookups/Treatment_Frequencies_Active.sql | 3 +++ ehr/resources/views/groupOverlaps.html | 2 +- ehr/src/org/labkey/ehr/EHRModule.java | 1 - ehr/src/org/labkey/ehr/EHRServiceImpl.java | 1 - 5 files changed, 5 insertions(+), 3 deletions(-) create mode 100644 EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql create mode 100644 ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql diff --git a/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql b/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql new file mode 100644 index 000000000..16b249449 --- /dev/null +++ b/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql @@ -0,0 +1 @@ +ALTER TABLE ehr_compliancedb.Employees ALTER COLUMN Notes TYPE NVARCHAR (4000); \ No newline at end of file diff --git a/ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql b/ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql new file mode 100644 index 000000000..aa215611b --- /dev/null +++ b/ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql @@ -0,0 +1,3 @@ +SELECT * +FROM ehr_lookups.treatment_frequency +WHERE active = 'true' \ No newline at end of file diff --git a/ehr/resources/views/groupOverlaps.html b/ehr/resources/views/groupOverlaps.html index 2f329e23c..084b07f48 100644 --- a/ehr/resources/views/groupOverlaps.html +++ b/ehr/resources/views/groupOverlaps.html @@ -154,7 +154,7 @@ renderTo: this.qwpDiv.id, schemaName: 'study', queryName: queryName, - title: 'Group Members Test', + title: 'Group Members', }; if (!start){ diff --git a/ehr/src/org/labkey/ehr/EHRModule.java b/ehr/src/org/labkey/ehr/EHRModule.java index 5ddcf1ef7..d3c90ea2d 100644 --- a/ehr/src/org/labkey/ehr/EHRModule.java +++ b/ehr/src/org/labkey/ehr/EHRModule.java @@ -256,7 +256,6 @@ public void moduleStartupComplete(ServletContext servletContext) EHRService.get().registerMoreActionsButton(new MarkCompletedButton(this, "study", "parentage", "End Selected Calls", true), "study", "parentage"); EHRService.get().registerMoreActionsButton(new ExcelImportButton(this, "study", "parentage", "Import Data"), "study", "parentage"); - EHRService.get().registerMoreActionsButton(new MarkCompletedButton(this, "study", "geneticAncestry", "End/Disable Selected", true), "study", "geneticAncestry"); EHRService.get().registerMoreActionsButton(new ExcelImportButton(this, "study", "geneticAncestry", "Import Data"), "study", "geneticAncestry"); EHRService.get().registerMoreActionsButton(new ProtocolEditButton(this, "ehr", "protocol"), "ehr", "protocol"); diff --git a/ehr/src/org/labkey/ehr/EHRServiceImpl.java b/ehr/src/org/labkey/ehr/EHRServiceImpl.java index 8154cc3e7..687a569fb 100644 --- a/ehr/src/org/labkey/ehr/EHRServiceImpl.java +++ b/ehr/src/org/labkey/ehr/EHRServiceImpl.java @@ -443,7 +443,6 @@ public void registerOptionalClinicalHistoryResources(Module module) EHRService.get().registerHistoryDataSource(new DefaultArrivalDataSource(module)); EHRService.get().registerHistoryDataSource(new DefaultAssignmentEndDataSource(module)); EHRService.get().registerHistoryDataSource(new DefaultBirthDataSource(module)); - // EHRService.get().registerHistoryDataSource(new DefaultClinicalRemarksDataSource(module)); EHRService.get().registerHistoryDataSource(new DefaultDeathsDataSource(module)); EHRService.get().registerHistoryDataSource(new DefaultDepartureDataSource(module)); EHRService.get().registerHistoryDataSource(new DefaultDrugsDataSource(module)); From 906bd4c4baafd145122aff37c7a81d180a1b19e1 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 14 Oct 2020 09:25:18 -0700 Subject: [PATCH 17/34] Code review change - use varchar for postgres instead of nvarchar --- .../dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql b/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql index 16b249449..2ee05593c 100644 --- a/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql +++ b/EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql @@ -1 +1 @@ -ALTER TABLE ehr_compliancedb.Employees ALTER COLUMN Notes TYPE NVARCHAR (4000); \ No newline at end of file +ALTER TABLE ehr_compliancedb.Employees ALTER COLUMN Notes TYPE VARCHAR (4000); \ No newline at end of file From 1179f0995c7f82af4c20244fd236171fcba7101f Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 20 Oct 2020 18:34:35 -0700 Subject: [PATCH 18/34] Code review change - remove expandRemarksColumn() that resets remarks column scale. --- .../labkey/ehr/table/DefaultEHRCustomizer.java | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java index da92c0f11..268835004 100644 --- a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java +++ b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java @@ -615,21 +615,6 @@ private void customizeStudyData(AbstractTableInfo ti) customizeButtonBar(ti); } - private void expandRemarksColumn(final AbstractTableInfo ti) - { - Dataset dataset = ((DatasetTable) ti).getDataset(); - Domain domain = dataset.getDomain(); - - // Hack the metadata for the length of the remark column, which has - // been altered in the DB so that it doesn't match with the standard - // "remark" property. See ONPRC ticket 33848 and EHRManager.ensureDatasetPropertyDescriptors() - TableInfo realTable = StorageProvisioner.getSchemaTableInfo(domain); - MutableColumnInfo remarkCol = (MutableColumnInfo) realTable.getColumn("remark"); - remarkCol.setLocked(false); - remarkCol.setScale(1000000); - remarkCol.setLocked(true); - } - private void customizeEncountersTable(final AbstractTableInfo ti) { appendEncountersCol(ti, "participants", "Participants", "encounter_participants_summary"); @@ -637,14 +622,11 @@ private void customizeEncountersTable(final AbstractTableInfo ti) appendEncountersCol(ti, "flags", "Flags", "encounter_flags_summary"); appendSNOMEDCol(ti); - - expandRemarksColumn(ti); } private void customizeGrossFindings(final AbstractTableInfo ti) { appendSNOMEDCol(ti); - expandRemarksColumn(ti); } private void customizeHistology(final AbstractTableInfo ti) From 2047202b17f89cdfff018c75fa2abdc71c3168ee Mon Sep 17 00:00:00 2001 From: Binal Date: Tue, 20 Oct 2020 19:22:59 -0700 Subject: [PATCH 19/34] -Replace hardcoded path with moduleProperty in sql queries. -Remove broken query study.currentBloodAvailable. -Add module property DCM_NHP_Resources_Container. -Update automated tests. --- .../external/onprc/ONPRC_BillingTest.java | 13 -------- .../AbstractGenericONPRC_EHRTest.java | 33 +++++++++++++++++++ .../test/tests/onprc_ehr/ONPRC_EHRTest.java | 2 ++ 3 files changed, 35 insertions(+), 13 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/external/onprc/ONPRC_BillingTest.java b/ehr/test/src/org/labkey/test/tests/external/onprc/ONPRC_BillingTest.java index 315a79a04..ad4b4e7b8 100644 --- a/ehr/test/src/org/labkey/test/tests/external/onprc/ONPRC_BillingTest.java +++ b/ehr/test/src/org/labkey/test/tests/external/onprc/ONPRC_BillingTest.java @@ -156,19 +156,6 @@ protected boolean skipStudyImportQueryValidation() return true; } - @Override - protected void setEHRModuleProperties(ModulePropertyValue... extraProps) - { - clickProject(PROJECT_NAME); - super._containerHelper.enableModule("ONPRC_Billing"); - super._containerHelper.enableModule("ONPRC_BillingPublic"); - super._containerHelper.enableModule("SLA"); - super.setEHRModuleProperties( - new ModulePropertyValue("ONPRC_Billing", "/" + getProjectName(), "BillingContainer", "/" + getContainerPath()), - new ModulePropertyValue("SLA", "/" + getProjectName(), "SLAContainer", "/" + getContainerPath()) - ); - } - @Override protected void populateInitialData() { diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java index 35cfea104..9f6a720af 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java @@ -15,6 +15,7 @@ */ package org.labkey.test.tests.onprc_ehr; +import com.sun.jdi.connect.ListeningConnector; import org.apache.commons.lang3.StringUtils; import org.json.simple.JSONObject; import org.labkey.remoteapi.CommandResponse; @@ -26,10 +27,13 @@ import org.labkey.remoteapi.query.SelectRowsCommand; import org.labkey.remoteapi.query.SelectRowsResponse; import org.labkey.test.Locator; +import org.labkey.test.ModulePropertyValue; import org.labkey.test.TestFileUtils; import org.labkey.test.WebTestHelper; +import org.labkey.test.params.FieldDefinition; import org.labkey.test.tests.ehr.AbstractGenericEHRTest; import org.labkey.test.util.Ext4Helper; +import org.labkey.test.util.ListHelper; import org.labkey.test.util.LogMethod; import org.labkey.test.util.PasswordUtil; import org.labkey.test.util.SqlserverOnlyTest; @@ -67,6 +71,8 @@ public abstract class AbstractGenericONPRC_EHRTest extends AbstractGenericEHRTes protected static String[] CAGES = {"A1", "B2", "A3"}; protected static Integer[] PROJECTS = {12345, 123456, 1234567}; + public ListHelper _listHelper; + @Override public String getModulePath() { @@ -91,6 +97,20 @@ protected EHRClientAPIHelper getApiHelper() return new EHRClientAPIHelper(this, getContainerPath()); } + @Override + protected void setEHRModuleProperties(ModulePropertyValue... extraProps) + { + log("Setting EHR Module Properties"); + clickProject(getProjectName()); + super._containerHelper.enableModule("ONPRC_Billing"); + super._containerHelper.enableModule("ONPRC_BillingPublic"); + super._containerHelper.enableModule("SLA"); + super.setEHRModuleProperties( + new ModulePropertyValue("ONPRC_Billing", "/" + getProjectName(), "BillingContainer", "/" + getContainerPath()), + new ModulePropertyValue("SLA", "/" + getProjectName(), "SLAContainer", "/" + getContainerPath()) + ); + } + @Override protected void importStudy() { @@ -124,6 +144,8 @@ protected void initProject() throws Exception { super.initProject("ONPRC EHR"); + createLabfeeNoChargeProjectsList(); + //this applies the standard property descriptors, creates indexes, etc. // NOTE: this currently will log an error from DatasetDefinition whenever we create a new column. This really isnt a bug, so ignore checkErrors(); @@ -137,6 +159,17 @@ protected void initProject() throws Exception cacheIds(Arrays.asList(MORE_ANIMAL_IDS)); } + private void createLabfeeNoChargeProjectsList() + { + _listHelper = new ListHelper(this); + ListHelper.ListColumn projectCol= new ListHelper.ListColumn("project", ListHelper.ListColumnType.Integer); + ListHelper.ListColumn startDateCol= new ListHelper.ListColumn("startDate", ListHelper.ListColumnType.DateAndTime); + ListHelper.ListColumn dateDisabledCol= new ListHelper.ListColumn("dateDisabled", ListHelper.ListColumnType.DateAndTime); + ListHelper.ListColumn createdDbCol= new ListHelper.ListColumn("Createdb", ListHelper.ListColumnType.Integer); + ListHelper.ListColumn notesCol= new ListHelper.ListColumn("Notes", ListHelper.ListColumnType.String); + _listHelper.createList(getProjectName(), "Labfee_NoChargeProjects", ListHelper.ListColumnType.Integer, "key", projectCol, startDateCol, dateDisabledCol, createdDbCol, notesCol); + } + protected void cacheIds(Collection ids) { beginAt(WebTestHelper.getBaseURL() + "/ehr/" + getContainerPath() + "/getDemographics.view?ids=" + StringUtils.join(ids, "&ids=")); diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 417674bf7..8695d4b53 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -108,6 +108,8 @@ public static void doSetup() throws Exception initTest.initProject(); initTest.createTestSubjects(); new RReportHelper(initTest).ensureRConfig(); + + initTest._containerHelper.enableModule("SLA"); } @Override From 99382f3b371a842a62c4a3381cb06fad78f88117 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 21 Oct 2020 00:57:07 -0700 Subject: [PATCH 20/34] Automated test updates --- .../labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 8695d4b53..ed0eac60e 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -50,6 +50,7 @@ import org.labkey.test.util.Maps; import org.labkey.test.util.PasswordUtil; import org.labkey.test.util.RReportHelper; +import org.labkey.test.util.SchemaHelper; import org.labkey.test.util.ehr.EHRClientAPIHelper; import org.labkey.test.util.ext4cmp.Ext4CmpRef; import org.labkey.test.util.ext4cmp.Ext4ComboRef; @@ -106,10 +107,12 @@ public static void doSetup() throws Exception ONPRC_EHRTest initTest = (ONPRC_EHRTest)getCurrentTest(); initTest.initProject(); + SchemaHelper schemaHelper = new SchemaHelper(initTest); + schemaHelper.createLinkedSchema(initTest.getProjectName(), null, "onprc_billing_public", "/" + initTest.getContainerPath(), "onprc_billing_public", null, null, null); + initTest.createTestSubjects(); new RReportHelper(initTest).ensureRConfig(); - initTest._containerHelper.enableModule("SLA"); } @Override @@ -118,6 +121,12 @@ protected boolean doSetUserPasswords() return true; } + @Override + protected boolean skipStudyImportQueryValidation() + { + return true; + } + @Test public void testBloodVolumeApi() throws Exception { From 1411dc850faffcd0d67d4c37c03099fba318f862 Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 21 Oct 2020 00:57:48 -0700 Subject: [PATCH 21/34] Code review changes --- ehr/resources/reports/schemas/study/Pedigree/Pedigree.r | 2 +- ehr/resources/views/groupOverlaps.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r index e4d260099..5d1bcce1e 100644 --- a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r +++ b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r @@ -16,7 +16,7 @@ library(Rlabkey) labkey.setCurlOptions(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE) -if ((length(labkey.data$id) == 0) || (is.na(labkey.data$dam) & is.na(labkey.data$sire))){ +if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam)) & is.na(labkey.data$sire)))){ png(filename="${imgout:myscatterplot}", width = 650, height = 150); plot(0, 0, type='n', xaxt='n', yaxt='n', bty='n', ann=FALSE ) title(main = "No pedigree data found for selected animal(s).", sub = NULL, xlab = NULL, ylab = NULL, diff --git a/ehr/resources/views/groupOverlaps.html b/ehr/resources/views/groupOverlaps.html index 084b07f48..f3c8a9515 100644 --- a/ehr/resources/views/groupOverlaps.html +++ b/ehr/resources/views/groupOverlaps.html @@ -154,7 +154,7 @@ renderTo: this.qwpDiv.id, schemaName: 'study', queryName: queryName, - title: 'Group Members', + title: 'Group Members' }; if (!start){ From 02997d287a82b5142f98d80b01a31a3e651be8fe Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 21 Oct 2020 23:44:23 -0700 Subject: [PATCH 22/34] Automated test fix for testArrivalApi(). (Fix for testBloodVolumeApi() wip) --- .../test/tests/onprc_ehr/ONPRC_EHRTest.java | 80 ++++++++++++++----- 1 file changed, 58 insertions(+), 22 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index ed0eac60e..1f55ca798 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -86,6 +86,7 @@ public class ONPRC_EHRTest extends AbstractGenericONPRC_EHRTest protected String PROJECT_NAME = "ONPRC_EHR_TestProject"; private boolean _hasCreatedBirthRecords = false; private String ANIMAL_HISTORY_URL = "/ehr/" + getProjectName() + "/animalHistory.view?"; + private int AvailableBloodVolume_rowId_starter = 100; @Override @@ -141,11 +142,40 @@ public void testBloodVolumeApi() throws Exception beginAt(WebTestHelper.buildURL("ehr", getContainerPath(), "primeDataEntryCache")); waitAndClickAndWait(Locator.lkButton("OK")); + addAvailableBloodVolumeData(SUBJECTS[0], SUBJECTS[1], SUBJECTS[2]); + testBloodDrawForAnimal(SUBJECTS[0]); testBloodDrawForAnimal(SUBJECTS[1]); testBloodDrawForAnimal(SUBJECTS[2]); } + private void addAvailableBloodVolumeData(String animalId1, String animalId2, String animalId3) throws Exception + { + goToProjectHome(); + + goToSchemaBrowser(); + viewQueryData("onprc_ehr", "AvailableBloodVolume"); + DataRegionTable availableBloodVolumeTable = new DataRegionTable("query", this); + + availableBloodVolumeTable.clickInsertNewRow(); + setFormElement(Locator.name("quf_id"), animalId1); + setFormElement(Locator.name("quf_dsrowid"), String.valueOf(++AvailableBloodVolume_rowId_starter)); + setFormElement(Locator.name("quf_ABV"), String.valueOf(5.5)); + clickButton("Submit"); + + availableBloodVolumeTable.clickInsertNewRow(); + setFormElement(Locator.name("quf_id"), animalId2); + setFormElement(Locator.name("quf_dsrowid"), String.valueOf(++AvailableBloodVolume_rowId_starter)); + setFormElement(Locator.name("quf_ABV"), String.valueOf(6.5)); + clickButton("Submit"); + + availableBloodVolumeTable.clickInsertNewRow(); + setFormElement(Locator.name("quf_id"), animalId3); + setFormElement(Locator.name("quf_dsrowid"), String.valueOf(++AvailableBloodVolume_rowId_starter)); + setFormElement(Locator.name("quf_ABV"), String.valueOf(7.5)); + clickButton("Submit"); + } + @Test public void testOverriddenActions() throws Exception { @@ -195,28 +225,28 @@ private void testBloodDrawForAnimal(@LoggedParam String animalId) throws Excepti startCal.add(Calendar.DATE, -15); startCal.add(Calendar.HOUR, 12); Object[][] bloodData = new Object[][]{ - {animalId, prepareDate(startCal.getTime(), -1, 0), 1.0, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 0, 0), 1.5, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 1, -4), 2.0, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 1, 0), 2.0, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 1, 4), 2.0, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 2, 0), 1.0, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 3, 1), 1.5, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 4, 0), 2.0, EHRQCState.REVIEW_REQUIRED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 4), 1.0, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 4, -2), 2.0, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 0), 1.0, EHRQCState.REVIEW_REQUIRED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 2), 1.0, EHRQCState.IN_PROGRESS.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 0), 1.0, EHRQCState.IN_PROGRESS.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval - 1, 0), 1.5, EHRQCState.REQUEST_PENDING.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval, 0), 2.0, EHRQCState.REQUEST_APPROVED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + 1, 0), 2.0, EHRQCState.REQUEST_PENDING.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), -1, 0), 1.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 0, 0), 1.5, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 1, -4), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 1, 0), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 1, 4), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 2, 0), 1.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 3, 1), 1.5, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 4, 0), 2.0, 1, EHRQCState.REVIEW_REQUIRED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 5, 4), 1.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 4, -2), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 5, 0), 1.0, 1, EHRQCState.REVIEW_REQUIRED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 5, 2), 1.0, 1, EHRQCState.IN_PROGRESS.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), 5, 0), 1.0, 1, EHRQCState.IN_PROGRESS.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), bloodDrawInterval - 1, 0), 1.5, 1, EHRQCState.REQUEST_PENDING.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), bloodDrawInterval, 0), 2.0, 1, EHRQCState.REQUEST_APPROVED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + 1, 0), 2.0, 1, EHRQCState.REQUEST_PENDING.label, generateGUID()}, //add draw far in future - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval - 1, 0), 2.0, EHRQCState.REQUEST_APPROVED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval + 1, 0), 2.0, EHRQCState.REQUEST_APPROVED.label, generateGUID()} + {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval - 1, 0), 2.0, 1, EHRQCState.REQUEST_APPROVED.label, generateGUID()}, + {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval + 1, 0), 2.0, 1, EHRQCState.REQUEST_APPROVED.label, generateGUID()} }; - PostCommand insertCommand = getApiHelper().prepareInsertCommand("study", "blood", "lsid", new String[]{"Id", "date", "quantity", "QCStateLabel", "objectid"}, bloodData); + PostCommand insertCommand = getApiHelper().prepareInsertCommand("study", "blood", "lsid", new String[]{"Id", "date", "quantity", "num_tubes", "QCStateLabel", "objectid"}, bloodData); getApiHelper().deleteAllRecords("study", "blood", new Filter("Id", animalId, Filter.Operator.EQUAL)); getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), insertCommand, getExtraContext()); @@ -243,7 +273,6 @@ private void testBloodDrawForAnimal(@LoggedParam String animalId) throws Excepti for (Object[] row : bloodData) { Date d = DateUtils.truncate(row[1], Calendar.DATE); - String qcLabel = (String) row[3]; Double vol = bloodByDay.containsKey(d) ? bloodByDay.get(d) : 0.0; //NOTE: we are including all QCStates @@ -846,14 +875,21 @@ public void testArrivalApi() throws Exception String quarrantineFlagId = ensureFlagExists("Surveillance", "Quarantine", null); String nonRestrictedFlagId = ensureFlagExists("Condition", "Nonrestricted", null); + log("Get AcquistionType rowid"); + SelectRowsCommand acquisitionTypeCmd = new SelectRowsCommand("ehr_lookups", "AcquistionType"); + acquisitionTypeCmd.setColumns(Arrays.asList("rowid", "value")); + acquisitionTypeCmd.addFilter(new Filter("value", "Acquired")); + Map acquisitionTypeResult= acquisitionTypeCmd.execute(getApiHelper().getConnection(), getContainerPath()).getRows().get(0); + Integer acqType = (Integer) acquisitionTypeResult.get("rowid"); + //insert into arrival log("Creating Ids"); Date birth = new Date(); Date arrivalDate = prepareDate(new Date(), -3, 0); getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), getApiHelper().prepareInsertCommand("study", "arrival", "lsid", - new String[]{"Id", "Date", "gender", "species", "geographic_origin", "birth", "initialRoom", "initialCage", "QCStateLabel"}, + new String[]{"Id", "Date", "gender", "species", "geographic_origin", "birth", "initialRoom", "initialCage", "QCStateLabel", "acquisitionType"}, new Object[][]{ - {arrivalId1, arrivalDate, "f", RHESUS, INDIAN, birth, ROOMS[0], CAGES[0], EHRQCState.COMPLETED.label} + {arrivalId1, arrivalDate, "f", RHESUS, INDIAN, birth, ROOMS[0], CAGES[0], EHRQCState.COMPLETED.label, acqType} } ), getExtraContext()); From 0a2ac0770bed7aa43b85864e3ade2995236244be Mon Sep 17 00:00:00 2001 From: Binal Date: Thu, 22 Oct 2020 11:27:01 -0700 Subject: [PATCH 23/34] Code review change - remove filtered query as fkTable, instead use a filter that will get applied during insert and update. --- .../queries/ehr_lookups/Treatment_Frequencies_Active.sql | 3 --- ehr/resources/queries/study/treatment_order.query.xml | 7 ++++++- 2 files changed, 6 insertions(+), 4 deletions(-) delete mode 100644 ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql diff --git a/ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql b/ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql deleted file mode 100644 index aa215611b..000000000 --- a/ehr/resources/queries/ehr_lookups/Treatment_Frequencies_Active.sql +++ /dev/null @@ -1,3 +0,0 @@ -SELECT * -FROM ehr_lookups.treatment_frequency -WHERE active = 'true' \ No newline at end of file diff --git a/ehr/resources/queries/study/treatment_order.query.xml b/ehr/resources/queries/study/treatment_order.query.xml index d86da1218..9dab559d4 100644 --- a/ehr/resources/queries/study/treatment_order.query.xml +++ b/ehr/resources/queries/study/treatment_order.query.xml @@ -60,8 +60,13 @@ Frequency ehr_lookups - Treatment_Frequencies_Active + treatment_frequency rowid + + + + + From 6d2a24da42f2ab047e0401fc8055be26bf0c83d5 Mon Sep 17 00:00:00 2001 From: Binal Date: Thu, 22 Oct 2020 11:52:46 -0700 Subject: [PATCH 24/34] Remove testBloodVolumeApi() - this test no longer relevant since LabKey is not managing the calculations & validations, it is now done by a third party tool. --- .../test/tests/onprc_ehr/ONPRC_EHRTest.java | 424 ------------------ 1 file changed, 424 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 1f55ca798..674bca797 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -128,54 +128,6 @@ protected boolean skipStudyImportQueryValidation() return true; } - @Test - public void testBloodVolumeApi() throws Exception - { - UpdateRowsCommand updateRowsCommand = new UpdateRowsCommand("ehr_lookups", "species"); - updateRowsCommand.addRow(Maps.of("common", "Rhesus", "blood_draw_interval", 21)); - updateRowsCommand.addRow(Maps.of("common", "Cynomolgus", "blood_draw_interval", 21)); - updateRowsCommand.addRow(Maps.of("common", "Marmoset", "blood_draw_interval", 21)); - SaveRowsResponse saveResponse = updateRowsCommand.execute(getApiHelper().getConnection(), getContainerPath()); - assertEquals(3, saveResponse.getRowsAffected().intValue()); - - //refresh caches to match new blood volumes. this really should be automatic on the server - beginAt(WebTestHelper.buildURL("ehr", getContainerPath(), "primeDataEntryCache")); - waitAndClickAndWait(Locator.lkButton("OK")); - - addAvailableBloodVolumeData(SUBJECTS[0], SUBJECTS[1], SUBJECTS[2]); - - testBloodDrawForAnimal(SUBJECTS[0]); - testBloodDrawForAnimal(SUBJECTS[1]); - testBloodDrawForAnimal(SUBJECTS[2]); - } - - private void addAvailableBloodVolumeData(String animalId1, String animalId2, String animalId3) throws Exception - { - goToProjectHome(); - - goToSchemaBrowser(); - viewQueryData("onprc_ehr", "AvailableBloodVolume"); - DataRegionTable availableBloodVolumeTable = new DataRegionTable("query", this); - - availableBloodVolumeTable.clickInsertNewRow(); - setFormElement(Locator.name("quf_id"), animalId1); - setFormElement(Locator.name("quf_dsrowid"), String.valueOf(++AvailableBloodVolume_rowId_starter)); - setFormElement(Locator.name("quf_ABV"), String.valueOf(5.5)); - clickButton("Submit"); - - availableBloodVolumeTable.clickInsertNewRow(); - setFormElement(Locator.name("quf_id"), animalId2); - setFormElement(Locator.name("quf_dsrowid"), String.valueOf(++AvailableBloodVolume_rowId_starter)); - setFormElement(Locator.name("quf_ABV"), String.valueOf(6.5)); - clickButton("Submit"); - - availableBloodVolumeTable.clickInsertNewRow(); - setFormElement(Locator.name("quf_id"), animalId3); - setFormElement(Locator.name("quf_dsrowid"), String.valueOf(++AvailableBloodVolume_rowId_starter)); - setFormElement(Locator.name("quf_ABV"), String.valueOf(7.5)); - clickButton("Submit"); - } - @Test public void testOverriddenActions() throws Exception { @@ -193,382 +145,6 @@ public void testOverriddenActions() throws Exception waitForElement(Locator.tagContainingText("a", "View Active Animal Assignments")); } - - private void testBloodDrawForAnimal(@LoggedParam String animalId) throws Exception - { - log("processing blood draws for: " + animalId); - - SelectRowsCommand select = new SelectRowsCommand("study", "demographics"); - select.addFilter(new Filter("Id", animalId, Filter.Operator.EQUAL)); - SelectRowsResponse resp = select.execute(getApiHelper().getConnection(), getContainerPath()); - Assert.assertEquals(1, resp.getRows().size()); - - Map demographicsRow = resp.getRows().get(0); - String species = (String) demographicsRow.get("species"); - - //find allowable volume - SelectRowsCommand select2 = new SelectRowsCommand("ehr_lookups", "species"); - select2.addFilter(new Filter("common", species, Filter.Operator.EQUAL)); - SelectRowsResponse resp2 = select2.execute(getApiHelper().getConnection(), getContainerPath()); - Assert.assertEquals(1, resp2.getRows().size()); - - Double bloodPerKg = (Double) resp2.getRows().get(0).get("blood_per_kg"); - Assert.assertTrue("Bad 'blood_per_kg': " + bloodPerKg, bloodPerKg > 0); - Double maxDrawPct = (Double) resp2.getRows().get(0).get("max_draw_pct"); - Assert.assertTrue("Bad 'max_draw_pct': " + maxDrawPct, maxDrawPct > 0); - Integer bloodDrawInterval = ((Double) resp2.getRows().get(0).get("blood_draw_interval")).intValue(); - Assert.assertEquals("Bad 'blood_draw_interval': " + bloodDrawInterval, 21, bloodDrawInterval.intValue()); - - log("Creating blood draws"); - Calendar startCal = Calendar.getInstance(); - startCal.setTime(DateUtils.truncate(new Date(), Calendar.DATE)); - startCal.add(Calendar.DATE, -15); - startCal.add(Calendar.HOUR, 12); - Object[][] bloodData = new Object[][]{ - {animalId, prepareDate(startCal.getTime(), -1, 0), 1.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 0, 0), 1.5, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 1, -4), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 1, 0), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 1, 4), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 2, 0), 1.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 3, 1), 1.5, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 4, 0), 2.0, 1, EHRQCState.REVIEW_REQUIRED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 4), 1.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 4, -2), 2.0, 1, EHRQCState.COMPLETED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 0), 1.0, 1, EHRQCState.REVIEW_REQUIRED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 2), 1.0, 1, EHRQCState.IN_PROGRESS.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), 5, 0), 1.0, 1, EHRQCState.IN_PROGRESS.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval - 1, 0), 1.5, 1, EHRQCState.REQUEST_PENDING.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval, 0), 2.0, 1, EHRQCState.REQUEST_APPROVED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + 1, 0), 2.0, 1, EHRQCState.REQUEST_PENDING.label, generateGUID()}, - //add draw far in future - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval - 1, 0), 2.0, 1, EHRQCState.REQUEST_APPROVED.label, generateGUID()}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval + 1, 0), 2.0, 1, EHRQCState.REQUEST_APPROVED.label, generateGUID()} - }; - - PostCommand insertCommand = getApiHelper().prepareInsertCommand("study", "blood", "lsid", new String[]{"Id", "date", "quantity", "num_tubes", "QCStateLabel", "objectid"}, bloodData); - getApiHelper().deleteAllRecords("study", "blood", new Filter("Id", animalId, Filter.Operator.EQUAL)); - getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), insertCommand, getExtraContext()); - - log("Creating weight records"); - Object[][] weightData = new Object[][]{ - {animalId, prepareDate(startCal.getTime(), -1, 0), 5.0, EHRQCState.COMPLETED.label}, - {animalId, prepareDate(startCal.getTime(), 5, 0), 4.0, EHRQCState.COMPLETED.label}, - {animalId, prepareDate(startCal.getTime(), 5, 1), 2.0, EHRQCState.COMPLETED.label}, - {animalId, prepareDate(startCal.getTime(), 10, 1), 6.0, EHRQCState.COMPLETED.label} - }; - Map weightByDay = new TreeMap<>(); - weightByDay.put(prepareDate(startCal.getTime(), -1, 0), 5.0); - weightByDay.put(prepareDate(startCal.getTime(), 5, 0), 3.0); - weightByDay.put(prepareDate(startCal.getTime(), 5, 1), 3.0); - weightByDay.put(prepareDate(startCal.getTime(), 10, 1), 6.0); - - PostCommand insertCommand2 = getApiHelper().prepareInsertCommand("study", "weight", "lsid", new String[]{"Id", "date", "weight", "QCStateLabel"}, weightData); - getApiHelper().deleteAllRecords("study", "weight", new Filter("Id", animalId, Filter.Operator.EQUAL)); - getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), insertCommand2, getExtraContext()); - - //validate results - //build map of daws by day: - Map bloodByDay = new TreeMap<>(); - for (Object[] row : bloodData) - { - Date d = DateUtils.truncate(row[1], Calendar.DATE); - Double vol = bloodByDay.containsKey(d) ? bloodByDay.get(d) : 0.0; - - //NOTE: we are including all QCStates - vol += (Double) row[2]; - - bloodByDay.put(d, vol); - } - - SelectRowsCommand select1 = new SelectRowsCommand("study", "blood"); - select1.setColumns(Arrays.asList("Id", "date", "quantity", "BloodRemaining/lastWeight", "BloodRemaining/allowableBlood", "BloodRemaining/previousBlood", "BloodRemaining/availableBlood", "BloodRemaining/minDate")); - Sort sort = new Sort("date"); - sort.setDirection(Sort.Direction.DESCENDING); - select1.setSorts(Arrays.asList(sort)); - select1.addFilter(new Filter("Id", animalId, Filter.Operator.EQUAL)); - SelectRowsResponse resp1 = select1.execute(getApiHelper().getConnection(), getContainerPath()); - - /*TODO: bloodSummary.sql and demographicsBloodSummary.sql seem to have changed functionality to only show the - current blood availability instead of historical and scheduled blood data as well. Removed parts of test - associated with these queries until we know if this is a desired change. - */ - - //validate blood draws, which really hits bloodSummary.sql -// for (Map row : resp1.getRows()) -// { -// Date rowDate = (Date) row.get("date"); -// -// Calendar minDate = Calendar.getInstance(); -// minDate.setTime(DateUtils.truncate(rowDate, Calendar.DATE)); -// minDate.add(Calendar.DATE, (-1 * bloodDrawInterval) + 1); -// -// Date rowMinDate = row.get("BloodRemaining/minDate") instanceof Date ? (Date) row.get("BloodRemaining/minDate") : _df.parse(row.get("BloodRemaining/minDate").toString()); -// Assert.assertEquals(minDate.getTime(), rowMinDate); -// -// Double lastWeight = null; -// for (Date weightDate : weightByDay.keySet()) -// { -// if (rowDate.getTime() >= DateUtils.truncate(weightDate, Calendar.DATE).getTime()) -// { -// lastWeight = weightByDay.get(weightDate); -// } -// } -// -// Assert.assertEquals(lastWeight, row.get("BloodRemaining/lastWeight")); -// Double previousBlood = 0.0; -// for (Date bloodDate : bloodByDay.keySet()) -// { -// //we want any draws GTE the min date considered and LTE the row's date -// if (bloodDate.getTime() >= minDate.getTime().getTime() && bloodDate.getTime() <= DateUtils.truncate(rowDate, Calendar.DATE).getTime()) -// { -// previousBlood += bloodByDay.get(bloodDate); -// } -// } -// Assert.assertEquals(previousBlood, row.get("BloodRemaining/previousBlood")); -// -// Double allowableBlood = lastWeight * bloodPerKg * maxDrawPct; -// Assert.assertEquals(allowableBlood, row.get("BloodRemaining/allowableBlood")); -// -// Double availableBlood = allowableBlood - previousBlood; -// Assert.assertEquals(availableBlood, row.get("BloodRemaining/availableBlood")); -// } - - //bloodDrawsByDay.sql - SelectRowsCommand select3 = new SelectRowsCommand("study", "bloodDrawsByDay"); - select3.setColumns(Arrays.asList("Id", "date", "quantity", "dropdate", "blood_draw_interval")); - select3.setSorts(Arrays.asList(sort)); - select3.addFilter(new Filter("Id", animalId, Filter.Operator.EQUAL)); - SelectRowsResponse resp3 = select3.execute(getApiHelper().getConnection(), getContainerPath()); - for (Map row : resp3.getRows()) - { - //note: some servers seem to return this as a string? - Date rowDate = (row.get("date") instanceof Date) ? (Date) row.get("date") : _df.parse(row.get("date").toString()); - Date rowDropDate = (row.get("dropdate") instanceof Date) ? (Date) row.get("dropdate") : _df.parse(row.get("dropdate").toString()); - - Calendar dropDate = Calendar.getInstance(); - dropDate.setTime(DateUtils.truncate(rowDate, Calendar.DATE)); - dropDate.add(Calendar.DATE, bloodDrawInterval); - Assert.assertEquals(dropDate.getTime(), rowDropDate); - Assert.assertEquals(bloodByDay.get(rowDate), row.get("quantity")); - Assert.assertEquals(bloodDrawInterval.doubleValue(), row.get("blood_draw_interval")); - } - - //currentBloodDraws.sql - SelectRowsCommand select4 = new SelectRowsCommand("study", "currentBloodDraws"); - select4.setColumns(Arrays.asList("Id", "date", "mostRecentWeight", "mostRecentWeightDate", "maxAllowableBlood", "bloodPrevious", "bloodFuture", "allowableFuture", "allowableBlood", "minDate", "maxDate")); - select4.setSorts(Arrays.asList(sort)); - select4.setQueryParameters(Maps.of("DATE_INTERVAL", bloodDrawInterval.toString())); - select4.addFilter(new Filter("Id", animalId, Filter.Operator.EQUAL)); - SelectRowsResponse resp4 = select4.execute(getApiHelper().getConnection(), getContainerPath()); - - for (Map row : resp4.getRows()) - { - //note: some servers seem to return this as a string? - Date rowDate = (row.get("date") instanceof Date) ? (Date) row.get("date") : _df.parse(row.get("date").toString()); - - Double lastWeight = null; - Date lastWeightDate = null; - for (Date weightDate : weightByDay.keySet()) - { - if (lastWeightDate == null || weightDate.getTime() >= lastWeightDate.getTime()) - { - lastWeightDate = weightDate; - lastWeight = weightByDay.get(weightDate); - } - } - Assert.assertEquals(lastWeight, row.get("mostRecentWeight")); - Assert.assertEquals(lastWeightDate, row.get("mostRecentWeightDate")); - - Double allowableBlood = lastWeight * bloodPerKg * maxDrawPct; - Assert.assertEquals(allowableBlood, row.get("maxAllowableBlood")); - - Double previousBlood = 0.0; - Double futureBlood = 0.0; - Calendar minDate = Calendar.getInstance(); - minDate.setTime(DateUtils.truncate(rowDate, Calendar.DATE)); - minDate.add(Calendar.DATE, -1 * bloodDrawInterval); - Assert.assertEquals(minDate.getTime(), row.get("minDate")); - - Calendar maxDate = Calendar.getInstance(); - maxDate.setTime(DateUtils.truncate(rowDate, Calendar.DATE)); - maxDate.add(Calendar.DATE, bloodDrawInterval); - Assert.assertEquals(maxDate.getTime(), row.get("maxDate")); - - for (Date bloodDate : bloodByDay.keySet()) - { - //we want any draws GTE the min date considered and LTE the row's date - if (bloodDate.getTime() > minDate.getTime().getTime() && bloodDate.getTime() <= DateUtils.truncate(rowDate, Calendar.DATE).getTime()) - { - previousBlood += bloodByDay.get(bloodDate); - } - - if (bloodDate.getTime() < maxDate.getTime().getTime() && bloodDate.getTime() >= DateUtils.truncate(rowDate, Calendar.DATE).getTime()) - { - futureBlood += bloodByDay.get(bloodDate); - } - } - Assert.assertEquals(previousBlood, row.get("bloodPrevious")); - Assert.assertEquals(futureBlood, row.get("bloodFuture")); - - Assert.assertEquals((allowableBlood - previousBlood), row.get("allowableBlood")); - Assert.assertEquals((allowableBlood - futureBlood), row.get("allowableFuture")); - } - - //demographicsBloodSummary.sql - SelectRowsCommand select5 = new SelectRowsCommand("study", "demographicsBloodSummary"); - select5.setColumns(Arrays.asList("Id", "mostRecentWeight", "mostRecentWeightDate", "availBlood", "bloodPrevious", "bloodFuture")); - select5.addFilter(new Filter("Id", animalId, Filter.Operator.EQUAL)); - SelectRowsResponse resp5 = select5.execute(getApiHelper().getConnection(), getContainerPath()); - - List dates = new ArrayList<>(weightByDay.keySet()); - Collections.sort(dates); - Date mostRecentWeightDate = dates.get(dates.size() - 1); - Double mostRecentWeight = weightByDay.get(mostRecentWeightDate); - Double allowableBlood = mostRecentWeight * bloodPerKg * maxDrawPct; -// for (Map row : resp5.getRows()) -// { -// Assert.assertEquals(mostRecentWeight, row.get("mostRecentWeight")); -// Assert.assertEquals(DateUtils.truncate(mostRecentWeightDate, Calendar.DATE), row.get("mostRecentWeightDate")); -// -// Calendar minDate = Calendar.getInstance(); -// minDate.setTime(DateUtils.truncate(new Date(), Calendar.DATE)); -// minDate.add(Calendar.DATE, -1 * bloodDrawInterval); -// -// Calendar maxDate = Calendar.getInstance(); -// maxDate.setTime(DateUtils.truncate(new Date(), Calendar.DATE)); -// maxDate.add(Calendar.DATE, bloodDrawInterval); -// -// Double previousBlood = 0.0; -// Double futureBlood = 0.0; -// for (Date bloodDate : bloodByDay.keySet()) -// { -// if (bloodDate.getTime() <= (new Date()).getTime() && bloodDate.getTime() >= minDate.getTime().getTime()) -// { -// previousBlood += bloodByDay.get(bloodDate); -// } -// -// if (bloodDate.getTime() > (new Date()).getTime() && bloodDate.getTime() < maxDate.getTime().getTime()) -// { -// futureBlood += bloodByDay.get(bloodDate); -// } -// } -// Assert.assertEquals(previousBlood, row.get("bloodPrevious")); -// Assert.assertEquals(futureBlood, row.get("bloodFuture")); -// -// Double availableBlood = allowableBlood - previousBlood; -// Assert.assertEquals(availableBlood, row.get("availBlood")); -// } - - log("checking validation errors"); - - //request that will exceed allowable - String[] bloodFields = new String[]{"Id", "date", "quantity", "QCStateLabel", "objectid", "_recordid"}; - getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "blood", bloodFields, new Object[][]{ - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval, 1), 73, EHRQCState.REQUEST_PENDING.label, generateGUID(), "recordID"} - }, Maps.of( - "quantity", Arrays.asList("ERROR: Blood volume of 73.0 (93.0 over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)"), - "num_tubes", Arrays.asList("ERROR: Blood volume of 73.0 (93.0 over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)") - ), Maps.of("targetQC", null)); - - //2 requests that will exceed the volume together - Double amount = 40.0; - Double warn1 = 20.0 + amount; - Double warn2 = 20.0 + amount + amount; - List expectedErrors = new ArrayList<>(); - expectedErrors.add("ERROR: Blood volume of 40.0 (" + warn2 + " over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)"); - if (warn1 > allowableBlood) - { - expectedErrors.add("ERROR: Blood volume of 40.0 (" + warn1 + " over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)"); - } - - getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "blood", bloodFields, new Object[][]{ - {animalId, _tf.format(prepareDate(startCal.getTime(), bloodDrawInterval, 1)), amount, EHRQCState.REQUEST_PENDING.label, generateGUID(), "recordID"}, - {animalId,_tf.format(prepareDate(startCal.getTime(), bloodDrawInterval, 1)), amount, EHRQCState.REQUEST_PENDING.label, generateGUID(), "recordID2"} - }, Maps.of( - "quantity", expectedErrors, - "num_tubes", expectedErrors - ), Maps.of("targetQC", null)); - - //use different date, which triggers different weight - Map additionalExtraContext = new HashMap<>(); - JSONObject weightInTransaction = new JSONObject(); - Double newWeight = 2.0; - Double newAllowableBlood = newWeight * bloodPerKg * maxDrawPct; - weightInTransaction.put(animalId, Arrays.asList(Maps.of("objectid", generateGUID(), "date", _tf.format(prepareDate(startCal.getTime(), bloodDrawInterval, 2)), "weight", newWeight))); - additionalExtraContext.put("weightInTransaction", weightInTransaction.toString()); - additionalExtraContext.put("targetQC", null); - - List expectedErrors2 = new ArrayList<>(); - expectedErrors2.add("ERROR: Blood volume of 40.0 (" + warn2 + " over " + bloodDrawInterval + " days) exceeds the allowable volume of " + newAllowableBlood + " mL (weight: " + newWeight + " kg)"); - if (warn1 > newAllowableBlood) - { - expectedErrors2.add("ERROR: Blood volume of 40.0 (" + warn1 + " over " + bloodDrawInterval + " days) exceeds the allowable volume of " + newAllowableBlood + " mL (weight: " + newWeight + " kg)"); - } - - getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "blood", bloodFields, new Object[][]{ - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval, 1), amount, EHRQCState.REQUEST_PENDING.label, generateGUID(), "recordID"}, - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval, 1), amount, EHRQCState.REQUEST_PENDING.label, generateGUID(), "recordID2"} - }, Maps.of( - "quantity", expectedErrors2, - "num_tubes", expectedErrors2 - ), additionalExtraContext); - - // try request right on date borders - getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "blood", bloodFields, new Object[][]{ - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval * 2, 1), 70.5, EHRQCState.COMPLETED.label, generateGUID(), "recordID"} - }, Maps.of( - "quantity", Arrays.asList( - "INFO: Blood volume of 70.5 (74.5 over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)" - ), - "num_tubes", Arrays.asList( - "INFO: Blood volume of 70.5 (74.5 over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)" - ), - "date", Arrays.asList("INFO: Date is in the future") - ), Maps.of("targetQC", null)); - - // this should fail - getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "blood", bloodFields, new Object[][]{ - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval * 2, 1), (allowableBlood - 5), EHRQCState.REQUEST_PENDING.label, generateGUID(), "recordID"} - }, Collections.emptyMap()); - - // advance one day and it should succeed, showing the draw drops off correctly - getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "blood", bloodFields, new Object[][]{ - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval * 2 + 1, 1), (allowableBlood - 5), EHRQCState.REQUEST_PENDING.label, generateGUID(), "recordID"} - }, Collections.emptyMap()); - - //insert record between two existing records. this record will itself be valid in either direction over the window; however, it will invalidate the previous draw - Map newRow = new HashMap<>(); - newRow.put("Id", animalId); - newRow.put("date", prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval - 2, 4)); - newRow.put("quantity", 2); - newRow.put("QCStateLabel", EHRQCState.REQUEST_APPROVED.label); - newRow.put("objectid", generateGUID()); - newRow.put("recordid", "recordID"); - - getApiHelper().insertRow("study", "blood", newRow, false); - - Map newRow2 = new HashMap<>(); - newRow2.put("Id", animalId); - newRow2.put("date", prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval + 2, 4)); - newRow2.put("quantity", 6); - newRow2.put("QCStateLabel", EHRQCState.REQUEST_APPROVED.label); - newRow2.put("objectid", generateGUID()); - newRow2.put("recordid", "recordID"); - - getApiHelper().insertRow("study", "blood", newRow2, false); - getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "blood", bloodFields, new Object[][]{ - {animalId, prepareDate(startCal.getTime(), bloodDrawInterval + bloodDrawInterval, 4), 62.0, EHRQCState.REQUEST_APPROVED.label, generateGUID(), "recordID"} - }, Maps.of( - "quantity", Arrays.asList( - "ERROR: Blood volume of 62.0 (74.0 over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)" - ), - "num_tubes", Arrays.asList( - "ERROR: Blood volume of 62.0 (74.0 over " + bloodDrawInterval + " days) exceeds the allowable volume of " + allowableBlood + " mL (weight: " + mostRecentWeight + " kg)" - ) - ), Maps.of("targetQC", null)); - } - private Pair generateProtocolAndProject() throws Exception { //create project From e3ea9e2b3011b6e81ffabca9061981e5c9d16353 Mon Sep 17 00:00:00 2001 From: Binal Date: Thu, 22 Oct 2020 21:27:57 -0700 Subject: [PATCH 25/34] Remove extra ')'. Test fixes. --- .../reports/schemas/study/Pedigree/Pedigree.r | 2 +- .../labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java | 10 +--------- .../labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java | 11 +++++++++++ 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r index 5d1bcce1e..5b51f09ce 100644 --- a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r +++ b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r @@ -16,7 +16,7 @@ library(Rlabkey) labkey.setCurlOptions(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE) -if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam)) & is.na(labkey.data$sire)))){ +if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.data$sire))) { png(filename="${imgout:myscatterplot}", width = 650, height = 150); plot(0, 0, type='n', xaxt='n', yaxt='n', bty='n', ann=FALSE ) title(main = "No pedigree data found for selected animal(s).", sub = NULL, xlab = NULL, ylab = NULL, diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 674bca797..46e2b104b 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -86,8 +86,6 @@ public class ONPRC_EHRTest extends AbstractGenericONPRC_EHRTest protected String PROJECT_NAME = "ONPRC_EHR_TestProject"; private boolean _hasCreatedBirthRecords = false; private String ANIMAL_HISTORY_URL = "/ehr/" + getProjectName() + "/animalHistory.view?"; - private int AvailableBloodVolume_rowId_starter = 100; - @Override protected String getProjectName() @@ -122,12 +120,6 @@ protected boolean doSetUserPasswords() return true; } - @Override - protected boolean skipStudyImportQueryValidation() - { - return true; - } - @Test public void testOverriddenActions() throws Exception { @@ -373,7 +365,7 @@ public void testProjectProtocolApi() throws Exception {null, projectName} }, Maps.of( "name", Arrays.asList( - "ERROR: There is already a project with the name: " + projectName + "ERROR: There is already an old project with the name in ehr: " + projectName ) )); } diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java index 990a3c91b..64fffbd6c 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java @@ -37,6 +37,7 @@ import org.labkey.test.util.LogMethod; import org.labkey.test.util.Maps; import org.labkey.test.util.PasswordUtil; +import org.labkey.test.util.SchemaHelper; import org.labkey.test.util.ext4cmp.Ext4CmpRef; import org.labkey.test.util.ext4cmp.Ext4ComboRef; import org.labkey.test.util.ext4cmp.Ext4FieldRef; @@ -77,6 +78,10 @@ public static void doSetup() throws Exception initTest.doCleanup(false); initTest.initProject(); + + SchemaHelper schemaHelper = new SchemaHelper(initTest); + schemaHelper.createLinkedSchema(initTest.getProjectName(), null, "onprc_billing_public", "/" + initTest.getContainerPath(), "onprc_billing_public", null, null, null); + initTest.createTestSubjects(); } @@ -86,6 +91,12 @@ protected boolean doSetUserPasswords() return true; } + @Override + protected boolean skipStudyImportQueryValidation() + { + return true; + } + @Test public void testBirthStatusApi() throws Exception { From 1c375ec04e8ef213d9364509b608b7888e736c38 Mon Sep 17 00:00:00 2001 From: Binal Date: Fri, 23 Oct 2020 00:10:33 -0700 Subject: [PATCH 26/34] Add values to Surgical Repairs template. Move skipStudyImportQueryValidation() to the parent class. --- .../test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java | 7 +++++++ .../org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java | 6 ------ 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java index 9f6a720af..a066c3562 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java @@ -97,6 +97,13 @@ protected EHRClientAPIHelper getApiHelper() return new EHRClientAPIHelper(this, getContainerPath()); } + + @Override + protected boolean skipStudyImportQueryValidation() + { + return true; + } + @Override protected void setEHRModuleProperties(ModulePropertyValue... extraProps) { diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java index 64fffbd6c..66961fbd2 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java @@ -91,12 +91,6 @@ protected boolean doSetUserPasswords() return true; } - @Override - protected boolean skipStudyImportQueryValidation() - { - return true; - } - @Test public void testBirthStatusApi() throws Exception { From 06b76579b0f6e6fd1fd23915c8c496933e2fbb74 Mon Sep 17 00:00:00 2001 From: Binal Date: Fri, 23 Oct 2020 22:42:23 -0700 Subject: [PATCH 27/34] Revert 'Add values to Surgical Repair template'. Use existing & functional utility code to get ehr_lookups.labwork_services store. Replace 'onprc-snomedtreatmentcombo' with 'ehr-snomedtreatmentcombo' (since the onprc one is not defined). Some cleanup. --- ehr/resources/web/ehr/DataEntryUtils.js | 23 ------------------- .../web/ehr/data/ClinpathRunsClientStore.js | 11 +-------- 2 files changed, 1 insertion(+), 33 deletions(-) diff --git a/ehr/resources/web/ehr/DataEntryUtils.js b/ehr/resources/web/ehr/DataEntryUtils.js index 5e926ea3b..531683cb1 100644 --- a/ehr/resources/web/ehr/DataEntryUtils.js +++ b/ehr/resources/web/ehr/DataEntryUtils.js @@ -823,29 +823,6 @@ EHR.DataEntryUtils = new function(){ return EHR._projectStore; }, - getProjectCodeStore: function(){ - //TODO: this really belongs in CNPRC_EHR module, not here. - if (EHR._projectStore) - return EHR._projectStore; - - var storeId = ['cnprc_ehr', 'project', 'projectCode'].join('||'); - - var ctx = EHR.Utils.getEHRContext(); - - EHR._projectStore = Ext4.StoreMgr.get(storeId) || new LABKEY.ext4.data.Store({ - type: 'labkey-store', - containerPath: ctx ? ctx['EHRStudyContainer'] : null, - schemaName: 'cnprc_ehr', - queryName: 'project', - columns: 'projectCode', - //filterArray: [LABKEY.Filter.create('enddate', null, LABKEY.Filter.Types.ISBLANK)], - sort: 'projectCode', - storeId: storeId, - autoLoad: true - }); - - return EHR._projectStore; - }, getDefaultClinicalProject: function(){ var ctx = EHR.Utils.getEHRContext(); diff --git a/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js b/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js index af881f471..9015bcf3d 100644 --- a/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js +++ b/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js @@ -35,16 +35,7 @@ Ext4.define('EHR.data.ClinpathRunsClientStore', { if (record.get('servicerequested')){ modifiedFieldNames = modifiedFieldNames || []; - var storeId = LABKEY.ext4.Util.getLookupStoreId({ - lookup: { - schemaName: 'ehr_lookups', - queryName: 'labwork_services', - keyColumn: 'servicename', - displayColumn: 'servicename' - } - }); - - var store = Ext4.StoreMgr.get(storeId); + var store = EHR.DataEntryUtils.getLabworkServicesStore(); if (!store){ LDK.Utils.logToServer({ message: 'Unable to find lookup store in ClinpathRunsClientStore' From 23308a2c02d080cbebd3ab4ecf3adf697ec7f141 Mon Sep 17 00:00:00 2001 From: Binal Date: Sat, 24 Oct 2020 00:02:46 -0700 Subject: [PATCH 28/34] Get LabworkServices store before getting 'servicerequested' (so the store is not loading when servicerequested is selected) --- ehr/resources/web/ehr/data/ClinpathRunsClientStore.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js b/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js index 9015bcf3d..d0eaa2858 100644 --- a/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js +++ b/ehr/resources/web/ehr/data/ClinpathRunsClientStore.js @@ -32,10 +32,10 @@ Ext4.define('EHR.data.ClinpathRunsClientStore', { }, onRecordUpdate: function(record, modifiedFieldNames){ + var store = EHR.DataEntryUtils.getLabworkServicesStore(); if (record.get('servicerequested')){ modifiedFieldNames = modifiedFieldNames || []; - var store = EHR.DataEntryUtils.getLabworkServicesStore(); if (!store){ LDK.Utils.logToServer({ message: 'Unable to find lookup store in ClinpathRunsClientStore' From 4171d413dd69702b9e51dec71926764f5e76c4d4 Mon Sep 17 00:00:00 2001 From: Binal Date: Sat, 24 Oct 2020 00:32:49 -0700 Subject: [PATCH 29/34] Skip "Billing Validation Notification" - this is broken on the server and not been run successfully by the client. --- ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 46e2b104b..469d8cfc5 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -1274,7 +1274,7 @@ public void testNotifications() //iterate all notifications and run them. log("running all notifications"); - List skippedNotifications = Arrays.asList("ETL Validation Notification"); + List skippedNotifications = Arrays.asList("ETL Validation Notification", "Billing Validation Notification"); //Skip "Billing Validation Notification" - this is broken on the server and not been run successfully by the client. int count = Locator.tagContainingText("a", "Run Report In Browser").findElements(getDriver()).size(); for (int i = 0; i < count; i++) From 5618ca47c7eacb343d8e931706d9b645aef66c51 Mon Sep 17 00:00:00 2001 From: Binal Date: Sun, 25 Oct 2020 21:36:30 -0700 Subject: [PATCH 30/34] Test fixes. Associate 'code' column with editorConfig for ehr_lookups.drug_defaults. --- ehr/resources/web/ehr/model/sources/Default.js | 8 +++++--- .../org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/ehr/resources/web/ehr/model/sources/Default.js b/ehr/resources/web/ehr/model/sources/Default.js index 12f89c3f8..a56d8549c 100644 --- a/ehr/resources/web/ehr/model/sources/Default.js +++ b/ehr/resources/web/ehr/model/sources/Default.js @@ -2649,9 +2649,11 @@ EHR.model.DataModelManager.registerMetadata('Default', { } }, 'ehr_lookups.drug_defaults': { - editorConfig: { - xtype: 'ehr-snomedcombo', - defaultSubset: 'All' + code: { + editorConfig: { + xtype: 'ehr-snomedcombo', + defaultSubset: 'All' + } }, category: { defaultValue: 'Standard' diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 469d8cfc5..24e8dadb1 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -1274,7 +1274,7 @@ public void testNotifications() //iterate all notifications and run them. log("running all notifications"); - List skippedNotifications = Arrays.asList("ETL Validation Notification", "Billing Validation Notification"); //Skip "Billing Validation Notification" - this is broken on the server and not been run successfully by the client. + List skippedNotifications = Arrays.asList("ETL Validation Notification", "Billing Validation Notification", "Pregnant NHPs Gestation Notification"); //Skip "Billing Validation Notification" - this is broken on the server and not been run successfully by the client. int count = Locator.tagContainingText("a", "Run Report In Browser").findElements(getDriver()).size(); for (int i = 0; i < count; i++) From 626f2cde23a68e8b225df7549588c89a04f5667e Mon Sep 17 00:00:00 2001 From: Binal Date: Wed, 28 Oct 2020 23:41:35 -0700 Subject: [PATCH 31/34] Remove skipStudyImportQueryValidation(), and other related refactor. Query updates (note: these queries still fail the validation, they are just partially updated/fixed). --- .../test/tests/ehr/AbstractEHRTest.java | 23 +++++++++++++++++ .../AbstractGenericONPRC_EHRTest.java | 25 +------------------ .../test/tests/onprc_ehr/ONPRC_EHRTest.java | 9 ------- .../test/tests/onprc_ehr/ONPRC_EHRTest2.java | 4 --- 4 files changed, 24 insertions(+), 37 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java b/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java index bac68b0af..71f32cc9e 100644 --- a/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java @@ -36,10 +36,12 @@ import org.labkey.test.pages.ehr.AnimalHistoryPage; import org.labkey.test.util.AdvancedSqlTest; import org.labkey.test.util.ApiPermissionsHelper; +import org.labkey.test.util.ListHelper; import org.labkey.test.util.LogMethod; import org.labkey.test.util.LoggedParam; import org.labkey.test.util.PasswordUtil; import org.labkey.test.util.PermissionsHelper; +import org.labkey.test.util.SchemaHelper; import org.labkey.test.util.ehr.EHRClientAPIHelper; import org.labkey.test.util.ehr.EHRTestHelper; import org.labkey.test.util.ext4cmp.Ext4CmpRef; @@ -363,6 +365,9 @@ protected void initProject(String type) throws Exception createUsersandPermissions();//note: we create the users prior to study import, b/c that user is used by TableCustomizers if(type.equals("CNPRC EHR") || type.equals("TNPRC EHR")) _setupHelper.loadEHRTableDefinitions(); + if(type.equals("ONPRC EHR")) + onprcSetupBeforeStudyUpload(); //this needs to happen before import study() below so that 'Validation Queries' step doesn't fail since the queries depend on setup in this method. + populateInitialData(); importStudy(); disableMiniProfiler(); @@ -373,6 +378,24 @@ protected void initProject(String type) throws Exception primeCaches(); } + private void onprcSetupBeforeStudyUpload() + { + //create onprc_billing_public linked schema + beginAt(getProjectName()); + SchemaHelper schemaHelper = new SchemaHelper(this); + schemaHelper.createLinkedSchema(this.getProjectName(), null, "onprc_billing_public", "/" + this.getContainerPath(), "onprc_billing_public", null, null, null); + + //create Labfee_NoChargeProjects + beginAt(getProjectName()); + ListHelper _listHelper = new ListHelper(this); + ListHelper.ListColumn projectCol= new ListHelper.ListColumn("project", ListHelper.ListColumnType.Integer); + ListHelper.ListColumn startDateCol= new ListHelper.ListColumn("startDate", ListHelper.ListColumnType.DateAndTime); + ListHelper.ListColumn dateDisabledCol= new ListHelper.ListColumn("dateDisabled", ListHelper.ListColumnType.DateAndTime); + ListHelper.ListColumn createdDbCol= new ListHelper.ListColumn("Createdb", ListHelper.ListColumnType.Integer); + ListHelper.ListColumn notesCol= new ListHelper.ListColumn("Notes", ListHelper.ListColumnType.String); + _listHelper.createList(getProjectName(), "Labfee_NoChargeProjects", ListHelper.ListColumnType.Integer, "key", projectCol, startDateCol, dateDisabledCol, createdDbCol, notesCol); + } + @LogMethod(quiet = true) protected void populate(@LoggedParam String tableLabel) { diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java index a066c3562..5001eebef 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java @@ -15,7 +15,6 @@ */ package org.labkey.test.tests.onprc_ehr; -import com.sun.jdi.connect.ListeningConnector; import org.apache.commons.lang3.StringUtils; import org.json.simple.JSONObject; import org.labkey.remoteapi.CommandResponse; @@ -30,7 +29,6 @@ import org.labkey.test.ModulePropertyValue; import org.labkey.test.TestFileUtils; import org.labkey.test.WebTestHelper; -import org.labkey.test.params.FieldDefinition; import org.labkey.test.tests.ehr.AbstractGenericEHRTest; import org.labkey.test.util.Ext4Helper; import org.labkey.test.util.ListHelper; @@ -71,8 +69,6 @@ public abstract class AbstractGenericONPRC_EHRTest extends AbstractGenericEHRTes protected static String[] CAGES = {"A1", "B2", "A3"}; protected static Integer[] PROJECTS = {12345, 123456, 1234567}; - public ListHelper _listHelper; - @Override public String getModulePath() { @@ -97,13 +93,6 @@ protected EHRClientAPIHelper getApiHelper() return new EHRClientAPIHelper(this, getContainerPath()); } - - @Override - protected boolean skipStudyImportQueryValidation() - { - return true; - } - @Override protected void setEHRModuleProperties(ModulePropertyValue... extraProps) { @@ -114,6 +103,7 @@ protected void setEHRModuleProperties(ModulePropertyValue... extraProps) super._containerHelper.enableModule("SLA"); super.setEHRModuleProperties( new ModulePropertyValue("ONPRC_Billing", "/" + getProjectName(), "BillingContainer", "/" + getContainerPath()), + new ModulePropertyValue("ONPRC_Billing", "/" + getProjectName(), "BillingContainer_Public", "/" + getContainerPath()), new ModulePropertyValue("SLA", "/" + getProjectName(), "SLAContainer", "/" + getContainerPath()) ); } @@ -151,8 +141,6 @@ protected void initProject() throws Exception { super.initProject("ONPRC EHR"); - createLabfeeNoChargeProjectsList(); - //this applies the standard property descriptors, creates indexes, etc. // NOTE: this currently will log an error from DatasetDefinition whenever we create a new column. This really isnt a bug, so ignore checkErrors(); @@ -166,17 +154,6 @@ protected void initProject() throws Exception cacheIds(Arrays.asList(MORE_ANIMAL_IDS)); } - private void createLabfeeNoChargeProjectsList() - { - _listHelper = new ListHelper(this); - ListHelper.ListColumn projectCol= new ListHelper.ListColumn("project", ListHelper.ListColumnType.Integer); - ListHelper.ListColumn startDateCol= new ListHelper.ListColumn("startDate", ListHelper.ListColumnType.DateAndTime); - ListHelper.ListColumn dateDisabledCol= new ListHelper.ListColumn("dateDisabled", ListHelper.ListColumnType.DateAndTime); - ListHelper.ListColumn createdDbCol= new ListHelper.ListColumn("Createdb", ListHelper.ListColumnType.Integer); - ListHelper.ListColumn notesCol= new ListHelper.ListColumn("Notes", ListHelper.ListColumnType.String); - _listHelper.createList(getProjectName(), "Labfee_NoChargeProjects", ListHelper.ListColumnType.Integer, "key", projectCol, startDateCol, dateDisabledCol, createdDbCol, notesCol); - } - protected void cacheIds(Collection ids) { beginAt(WebTestHelper.getBaseURL() + "/ehr/" + getContainerPath() + "/getDemographics.view?ids=" + StringUtils.join(ids, "&ids=")); diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index 24e8dadb1..d5b7ed68e 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -19,15 +19,12 @@ import org.apache.commons.lang3.time.DateUtils; import org.apache.commons.lang3.tuple.Pair; import org.json.simple.JSONArray; -import org.json.simple.JSONObject; import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; import org.junit.experimental.categories.Category; -import org.labkey.remoteapi.PostCommand; import org.labkey.remoteapi.query.Filter; import org.labkey.remoteapi.query.InsertRowsCommand; -import org.labkey.remoteapi.query.SaveRowsResponse; import org.labkey.remoteapi.query.SelectRowsCommand; import org.labkey.remoteapi.query.SelectRowsResponse; import org.labkey.remoteapi.query.Sort; @@ -46,7 +43,6 @@ import org.labkey.test.util.DataRegionTable; import org.labkey.test.util.Ext4Helper; import org.labkey.test.util.LogMethod; -import org.labkey.test.util.LoggedParam; import org.labkey.test.util.Maps; import org.labkey.test.util.PasswordUtil; import org.labkey.test.util.RReportHelper; @@ -64,7 +60,6 @@ import java.time.LocalDateTime; import java.time.format.DateTimeFormatter; import java.time.temporal.ChronoUnit; -import java.time.temporal.TemporalUnit; import java.util.ArrayList; import java.util.Arrays; import java.util.Calendar; @@ -75,7 +70,6 @@ import java.util.List; import java.util.Map; import java.util.Set; -import java.util.TreeMap; import static org.junit.Assert.assertEquals; @@ -106,9 +100,6 @@ public static void doSetup() throws Exception ONPRC_EHRTest initTest = (ONPRC_EHRTest)getCurrentTest(); initTest.initProject(); - SchemaHelper schemaHelper = new SchemaHelper(initTest); - schemaHelper.createLinkedSchema(initTest.getProjectName(), null, "onprc_billing_public", "/" + initTest.getContainerPath(), "onprc_billing_public", null, null, null); - initTest.createTestSubjects(); new RReportHelper(initTest).ensureRConfig(); diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java index 66961fbd2..8fd60d936 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java @@ -78,10 +78,6 @@ public static void doSetup() throws Exception initTest.doCleanup(false); initTest.initProject(); - - SchemaHelper schemaHelper = new SchemaHelper(initTest); - schemaHelper.createLinkedSchema(initTest.getProjectName(), null, "onprc_billing_public", "/" + initTest.getContainerPath(), "onprc_billing_public", null, null, null); - initTest.createTestSubjects(); } From 78f6cdd85cd07c3a90c9c7a2289ccb0a9d6f11cb Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Thu, 29 Oct 2020 16:04:58 -0700 Subject: [PATCH 32/34] Clean up queries - delete defunct queries, add missing lists and columns, fix up XML --- .../test/tests/ehr/AbstractEHRTest.java | 45 ++++++++++++++++++- .../AbstractGenericONPRC_EHRTest.java | 4 +- 2 files changed, 46 insertions(+), 3 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java b/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java index 71f32cc9e..606531c24 100644 --- a/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java @@ -387,13 +387,56 @@ private void onprcSetupBeforeStudyUpload() //create Labfee_NoChargeProjects beginAt(getProjectName()); - ListHelper _listHelper = new ListHelper(this); + ListHelper.ListColumn projectCol= new ListHelper.ListColumn("project", ListHelper.ListColumnType.Integer); ListHelper.ListColumn startDateCol= new ListHelper.ListColumn("startDate", ListHelper.ListColumnType.DateAndTime); ListHelper.ListColumn dateDisabledCol= new ListHelper.ListColumn("dateDisabled", ListHelper.ListColumnType.DateAndTime); ListHelper.ListColumn createdDbCol= new ListHelper.ListColumn("Createdb", ListHelper.ListColumnType.Integer); ListHelper.ListColumn notesCol= new ListHelper.ListColumn("Notes", ListHelper.ListColumnType.String); _listHelper.createList(getProjectName(), "Labfee_NoChargeProjects", ListHelper.ListColumnType.Integer, "key", projectCol, startDateCol, dateDisabledCol, createdDbCol, notesCol); + + _listHelper.createList(getProjectName(), "GeneticValue", ListHelper.ListColumnType.String, "Id", + new ListHelper.ListColumn("meanKinship", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("zscore", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("genomeUniqueness", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("totalOffspring", ListHelper.ListColumnType.Integer), + new ListHelper.ListColumn("livingOffspring", ListHelper.ListColumnType.Integer), + new ListHelper.ListColumn("assignments", ListHelper.ListColumnType.Integer), + new ListHelper.ListColumn("condition", ListHelper.ListColumnType.String), + new ListHelper.ListColumn("import", ListHelper.ListColumnType.String), + new ListHelper.ListColumn("value", ListHelper.ListColumnType.String), + new ListHelper.ListColumn("rank", ListHelper.ListColumnType.Integer) + ); + + _listHelper.createList(getProjectName(), "Special_Aliases", ListHelper.ListColumnType.AutoInteger, "Key", + new ListHelper.ListColumn("Category", ListHelper.ListColumnType.String), + new ListHelper.ListColumn("Alias", ListHelper.ListColumnType.String)); + + // Fake up an external schema connection for "dbo" via a list and a linked schema + _listHelper.createList(getProjectName(), "Rpt_ChargesProjection", ListHelper.ListColumnType.AutoInteger, "RowId", + new ListHelper.ListColumn("ChargeId", ListHelper.ListColumnType.Integer), + new ListHelper.ListColumn("UnitCost", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year1", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year2", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year3", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year4", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year5", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year6", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year7", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("year8", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate1", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate2", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate3", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate4", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate5", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate6", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate7", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate8", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("Aprate9", ListHelper.ListColumnType.Decimal), + new ListHelper.ListColumn("PostedDate", ListHelper.ListColumnType.DateAndTime) + ); + schemaHelper.createLinkedSchema(this.getProjectName(), null, "dbo", "/" + this.getContainerPath(), null, "lists", null, null); + } @LogMethod(quiet = true) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java index 5001eebef..2d9f6430f 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java @@ -31,7 +31,6 @@ import org.labkey.test.WebTestHelper; import org.labkey.test.tests.ehr.AbstractGenericEHRTest; import org.labkey.test.util.Ext4Helper; -import org.labkey.test.util.ListHelper; import org.labkey.test.util.LogMethod; import org.labkey.test.util.PasswordUtil; import org.labkey.test.util.SqlserverOnlyTest; @@ -104,7 +103,8 @@ protected void setEHRModuleProperties(ModulePropertyValue... extraProps) super.setEHRModuleProperties( new ModulePropertyValue("ONPRC_Billing", "/" + getProjectName(), "BillingContainer", "/" + getContainerPath()), new ModulePropertyValue("ONPRC_Billing", "/" + getProjectName(), "BillingContainer_Public", "/" + getContainerPath()), - new ModulePropertyValue("SLA", "/" + getProjectName(), "SLAContainer", "/" + getContainerPath()) + new ModulePropertyValue("SLA", "/" + getProjectName(), "SLAContainer", "/" + getContainerPath()), + new ModulePropertyValue("ONPRC_EHR", "/" + getProjectName(), "DCM_NHP_Resources_Container", "/" + getContainerPath()) ); } From 7375737f0be3d98b706b9d3242eec3abea2cc514 Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Fri, 30 Oct 2020 09:30:25 -0700 Subject: [PATCH 33/34] Fix ONPRC_EHRTest2.testArrivalForm --- .../test/tests/onprc_ehr/ONPRC_EHRTest2.java | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java index 8fd60d936..850f880b3 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java @@ -501,7 +501,7 @@ public void testArrivalForm() throws Exception { _helper.goToTaskForm("Arrival", "Submit Final", false); - waitAndClick(Ext4Helper.Locators.ext4Button("Lock Entry")); + waitAndClick(Ext4Helper.Locators.ext4Button("Enable the form for data entry")); waitForElement(Ext4Helper.Locators.ext4Button("Submit Final"), WAIT_FOR_PAGE * 2); _ext4Helper.queryOne("button[text='Submit Final']", Ext4CmpRef.class).waitForEnabled(); @@ -536,6 +536,13 @@ public void testArrivalForm() throws Exception sourceField.waitForStoreLoad(); sourceField.setComboByDisplayValue(source); + String acquisitionType = "Acquired"; + _helper.toggleBulkEditField("Acquisition Type"); + + Ext4ComboRef acquisitionTypeField = _ext4Helper.queryOne("window field[fieldLabel='Acquisition Type']", Ext4ComboRef.class); + acquisitionTypeField.waitForStoreLoad(); + acquisitionTypeField.setComboByDisplayValue(acquisitionType); + String gender = "female"; _helper.toggleBulkEditField("Gender"); _ext4Helper.queryOne("window field[fieldLabel=Gender]", Ext4ComboRef.class).setComboByDisplayValue(gender); @@ -573,12 +580,16 @@ public void testArrivalForm() throws Exception waitAndClick(_helper.getDataEntryButton("Submit Final")); waitForElement(Ext4Helper.Locators.window("Finalize Birth/Arrival Form")); - waitAndClick(WAIT_FOR_JAVASCRIPT, Ext4Helper.Locators.window("Finalize Birth/Arrival Form").append(Ext4Helper.Locators.ext4Button("Yes")), WAIT_FOR_PAGE * 2); + Locator finalizeOKButton = Ext4Helper.Locators.window("Finalize Birth/Arrival Form").append(Ext4Helper.Locators.ext4Button("Yes")); + waitForElement(finalizeOKButton, WAIT_FOR_JAVASCRIPT); + click(finalizeOKButton); + + waitAndClick(WAIT_FOR_JAVASCRIPT * 2, Ext4Helper.Locators.window("Success").append(Ext4Helper.Locators.ext4Button("No")), WAIT_FOR_PAGE); waitForElement(Locator.tagWithText("a", "Enter New Data")); _helper.goToTaskForm("Arrival", "Submit Final", false); - waitAndClick(Ext4Helper.Locators.ext4Button("Lock Entry")); + waitAndClick(Ext4Helper.Locators.ext4Button("Enable the form for data entry")); waitForElement(Ext4Helper.Locators.ext4Button("Submit Final"), WAIT_FOR_PAGE * 2); _ext4Helper.queryOne("button[text='Submit Final']", Ext4CmpRef.class).waitForEnabled(); From 1c90aac1a1e9b9af7edda344d64416dbb4458054 Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Fri, 30 Oct 2020 10:26:59 -0700 Subject: [PATCH 34/34] Fix ONPRC_EHRTest.testNecropsyRequestFlow --- .../labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java index d5b7ed68e..58c513905 100644 --- a/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java @@ -23,6 +23,7 @@ import org.junit.BeforeClass; import org.junit.Test; import org.junit.experimental.categories.Category; +import org.labkey.remoteapi.CommandException; import org.labkey.remoteapi.query.Filter; import org.labkey.remoteapi.query.InsertRowsCommand; import org.labkey.remoteapi.query.SelectRowsCommand; @@ -57,6 +58,7 @@ import org.openqa.selenium.WebElement; import java.io.File; +import java.io.IOException; import java.time.LocalDateTime; import java.time.format.DateTimeFormatter; import java.time.temporal.ChronoUnit; @@ -131,7 +133,7 @@ public void testOverriddenActions() throws Exception private Pair generateProtocolAndProject() throws Exception { //create project - String protocolTitle = generateGUID(); + String protocolTitle = generateGUID(); InsertRowsCommand protocolCommand = new InsertRowsCommand("ehr", "protocol"); protocolCommand.addRow(Maps.of("protocol", null, "title", protocolTitle)); protocolCommand.execute(getApiHelper().getConnection(), getContainerPath()); @@ -1768,7 +1770,7 @@ public void testClinicalHistoryPanelOptions(){ } @Test - public void testNecropsyRequestFlow() + public void testNecropsyRequestFlow() throws IOException, CommandException { String animalId = "12345"; LocalDateTime now = LocalDateTime.now(); @@ -1779,6 +1781,11 @@ public void testNecropsyRequestFlow() DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd"); String tissue = "AMNION (T-88300)"; + // Insert a row so we can select a charge unit in the form + InsertRowsCommand protocolCommand = new InsertRowsCommand("onprc_billing", "chargeUnits"); + protocolCommand.addRow(Maps.of("chargetype", "ChargeUnit1", "servicecenter", "ServiceCenter1", "shownInProcedures", true, "active", true)); + protocolCommand.execute(getApiHelper().getConnection(), getContainerPath()); + log("Begin the test with entry data page"); EnterDataPage enterData = EnterDataPage.beginAt(this, getContainerPath()); enterData.waitAndClickAndWait(Locator.linkWithText("Necropsy Request")); @@ -1793,6 +1800,7 @@ public void testNecropsyRequestFlow() clickButton("Submit",0); _ext4Helper.selectComboBoxItem("Type:", Ext4Helper.TextMatchTechnique.CONTAINS,type); setNecropsYFormElement("chargetype", chargeType); + _ext4Helper.selectComboBoxItem("Charge Unit:", Ext4Helper.TextMatchTechnique.CONTAINS, "ChargeUnit1"); _ext4Helper.selectComboBoxItem("Procedure:", Ext4Helper.TextMatchTechnique.CONTAINS, procedureid); LocalDateTime tomorrow = now.plus(1, ChronoUnit.DAYS);