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Merged
bbimber merged 5 commits into from
Dec 21, 2023
Merged

Merge discvr-23.11 to develop #187

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7f7d5a3
Add MCC option to abstain
bbimber Dec 14, 2023
9f85d3c
Add support for mGAP annotations to supply InDefaultFields (#145)
bbimber Dec 20, 2023
e9151dd
Add column to report source folder in MCC query
bbimber Dec 20, 2023
959890d
Bugfix to logic when boolean values are null for AnnotationModel
bbimber Dec 20, 2023
d1d9bcb
Merge discvr-23.11 to develop
bbimber Dec 21, 2023
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1 change: 1 addition & 0 deletions mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql
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@@ -0,0 +1 @@
ALTER TABLE mGAP.annotations ADD inDefaultColumns boolean;
1 change: 1 addition & 0 deletions mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql
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@@ -0,0 +1 @@
ALTER TABLE mGAP.annotations ADD inDefaultColumns bit;
3 changes: 3 additions & 0 deletions mGAP/resources/schemas/mgap.xml
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Expand Up @@ -1224,6 +1224,9 @@
<column columnName="allowableValues">
<columnTitle>Allowable Values</columnTitle>
</column>
<column columnName="inDefaultColumns">
<columnTitle>In Default Columns?</columnTitle>
</column>
<column columnName="container">
<isHidden>true</isHidden>
</column>
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15 changes: 14 additions & 1 deletion mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java
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Expand Up @@ -17,6 +17,7 @@ public class AnnotationModel
private String _formatString;
private Boolean _hidden = false;
private Boolean _isIndexed = false;
private Boolean _inDefaultColumns = false;
private String _allowableValues;

public AnnotationModel()
Expand Down Expand Up @@ -166,7 +167,8 @@ public void setHidden(Boolean hidden)

public boolean isIndexed()
{
return _isIndexed == null || _isIndexed;
// Defaults to false when null
return _isIndexed != null && _isIndexed;
}

public void setIndexed(Boolean indexed)
Expand All @@ -183,4 +185,15 @@ public void setAllowableValues(String allowableValues)
{
_allowableValues = allowableValues;
}

public Boolean isInDefaultColumns()
{
// Defaults to false when null
return _inDefaultColumns != null && _inDefaultColumns;
}

public void setInDefaultColumns(Boolean inDefaultColumns)
{
_inDefaultColumns = inDefaultColumns;
}
}
5 changes: 5 additions & 0 deletions mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java
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Expand Up @@ -50,6 +50,11 @@ else if (ams.size() > 1)
field.setIndexed(true);
}

if (am.isInDefaultColumns())
{
field.setInDefaultColumns(true);
}

if (StringUtils.trimToNull(am.getDescription()) != null)
{
field.setDescription(am.getDescription());
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1 change: 1 addition & 0 deletions mGAP/src/org/labkey/mgap/mGAPController.java
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Expand Up @@ -1209,6 +1209,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
getOptionalField(line, header, "FormatString", row, "formatString");
getOptionalField(line, header, "AllowableValues", row, "allowableValues");
getOptionalField(line, header, "IsIndexed", row, "isIndexed");
getOptionalField(line, header, "InDefaultColumns", row, "inDefaultColumns");

toAdd.add(row);
}
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2 changes: 1 addition & 1 deletion mGAP/src/org/labkey/mgap/mGAPManager.java
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Expand Up @@ -99,7 +99,7 @@ public Set<User> getNotificationUsers()

if (u == null)
{
_log.error("Unknown user registered for mGAP notifcations: " + username);
_log.error("Unknown user registered for mGAP notifications: " + username);
}

if (u != null)
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2 changes: 1 addition & 1 deletion mGAP/src/org/labkey/mgap/mGAPModule.java
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Expand Up @@ -74,7 +74,7 @@ public String getName()
@Override
public Double getSchemaVersion()
{
return 16.70;
return 16.71;
}

@Override
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3 changes: 2 additions & 1 deletion mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql
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@@ -1,7 +1,8 @@
SELECT

m.Id,
GROUP_CONCAT(distinct m.originalId, ',') as originalIds
GROUP_CONCAT(distinct m.originalId, ',') as originalIds,
GROUP_CONCAT(distinct m.container.name, ',') as folders

FROM mcc.aggregatedDemographics m

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1 change: 1 addition & 0 deletions mcc/src/client/RequestReview/components/RabReviewForm.tsx
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Expand Up @@ -117,6 +117,7 @@ export default function RabReviewForm(props: {requestId: string}) {
<MenuItem value={"I recommend this proposal"}>I recommend this proposal</MenuItem>
<MenuItem value={"I recommend this proposal with conditions"}>I recommend this proposal with conditions</MenuItem>
<MenuItem value={"I do not recommend this proposal"}>I do not recommend this proposal</MenuItem>
<MenuItem value={"I abstain from voting"}>I abstain from voting</MenuItem>
</Select>
</TableCell>
</TableRow>
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