diff --git a/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql b/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql new file mode 100644 index 000000000..9223274b1 --- /dev/null +++ b/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql @@ -0,0 +1 @@ +ALTER TABLE mGAP.variantCatalogReleases ADD inDefaultColumns boolean; \ No newline at end of file diff --git a/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql new file mode 100644 index 000000000..1f2f3c5c3 --- /dev/null +++ b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql @@ -0,0 +1 @@ +ALTER TABLE mGAP.variantCatalogReleases ADD inDefaultColumns bit; \ No newline at end of file diff --git a/mGAP/resources/schemas/mgap.xml b/mGAP/resources/schemas/mgap.xml index 3614aa3a3..08f52c43e 100644 --- a/mGAP/resources/schemas/mgap.xml +++ b/mGAP/resources/schemas/mgap.xml @@ -1224,6 +1224,9 @@ Allowable Values + + In Default Columns? + true diff --git a/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java b/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java index 395c9486e..60b7e87e5 100644 --- a/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java +++ b/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java @@ -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() @@ -183,4 +184,14 @@ public void setAllowableValues(String allowableValues) { _allowableValues = allowableValues; } + + public Boolean isInDefaultColumns() + { + return _inDefaultColumns; + } + + public void setInDefaultColumns(Boolean inDefaultColumns) + { + _inDefaultColumns = inDefaultColumns; + } } diff --git a/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java b/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java index b70428a91..b1ab44524 100644 --- a/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java +++ b/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java @@ -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()); diff --git a/mGAP/src/org/labkey/mgap/mGAPController.java b/mGAP/src/org/labkey/mgap/mGAPController.java index 657cfcb0a..0adbb2d31 100644 --- a/mGAP/src/org/labkey/mgap/mGAPController.java +++ b/mGAP/src/org/labkey/mgap/mGAPController.java @@ -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); } diff --git a/mGAP/src/org/labkey/mgap/mGAPManager.java b/mGAP/src/org/labkey/mgap/mGAPManager.java index e2b0679d2..840d419ec 100644 --- a/mGAP/src/org/labkey/mgap/mGAPManager.java +++ b/mGAP/src/org/labkey/mgap/mGAPManager.java @@ -99,7 +99,7 @@ public Set 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) diff --git a/mGAP/src/org/labkey/mgap/mGAPModule.java b/mGAP/src/org/labkey/mgap/mGAPModule.java index 0a2036a1e..6bdc5af3c 100644 --- a/mGAP/src/org/labkey/mgap/mGAPModule.java +++ b/mGAP/src/org/labkey/mgap/mGAPModule.java @@ -74,7 +74,7 @@ public String getName() @Override public Double getSchemaVersion() { - return 16.70; + return 16.71; } @Override