From 7f7d5a362d40c816054da599269eea78e6b16eab Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 14 Dec 2023 11:17:06 -0800 Subject: [PATCH 1/4] Add MCC option to abstain --- mcc/src/client/RequestReview/components/RabReviewForm.tsx | 1 + 1 file changed, 1 insertion(+) diff --git a/mcc/src/client/RequestReview/components/RabReviewForm.tsx b/mcc/src/client/RequestReview/components/RabReviewForm.tsx index 581fef49f..f6dbe10d2 100644 --- a/mcc/src/client/RequestReview/components/RabReviewForm.tsx +++ b/mcc/src/client/RequestReview/components/RabReviewForm.tsx @@ -117,6 +117,7 @@ export default function RabReviewForm(props: {requestId: string}) { I recommend this proposal I recommend this proposal with conditions I do not recommend this proposal + I abstain from voting From 9f85d3c73b69440279317a8a7bb9c754e17d1ec4 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 20 Dec 2023 07:53:33 -0600 Subject: [PATCH 2/4] Add support for mGAP annotations to supply InDefaultFields (#145) * Add support for mGAP annotations to supply InDefaultFields --- .../schemas/dbscripts/postgresql/mgap-16.70-16.71.sql | 1 + .../schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql | 1 + mGAP/resources/schemas/mgap.xml | 3 +++ mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java | 11 +++++++++++ .../org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java | 5 +++++ mGAP/src/org/labkey/mgap/mGAPController.java | 1 + mGAP/src/org/labkey/mgap/mGAPManager.java | 2 +- mGAP/src/org/labkey/mgap/mGAPModule.java | 2 +- 8 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql create mode 100644 mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql 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..0c106116f --- /dev/null +++ b/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql @@ -0,0 +1 @@ +ALTER TABLE mGAP.annotations 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..982d13c31 --- /dev/null +++ b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql @@ -0,0 +1 @@ +ALTER TABLE mGAP.annotations 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 From e9151dd7c1499adfca35ed52684b3eb67adb0ea0 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 20 Dec 2023 05:54:33 -0800 Subject: [PATCH 3/4] Add column to report source folder in MCC query --- mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql b/mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql index 93d33162c..16515aa66 100644 --- a/mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql +++ b/mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql @@ -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 From 959890df5cdbf7783895aebfa33f28287cdedc8c Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 20 Dec 2023 09:44:18 -0800 Subject: [PATCH 4/4] Bugfix to logic when boolean values are null for AnnotationModel --- mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java b/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java index 60b7e87e5..40ac644d9 100644 --- a/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java +++ b/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java @@ -167,7 +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) @@ -187,7 +188,8 @@ public void setAllowableValues(String allowableValues) public Boolean isInDefaultColumns() { - return _inDefaultColumns; + // Defaults to false when null + return _inDefaultColumns != null && _inDefaultColumns; } public void setInDefaultColumns(Boolean inDefaultColumns)