diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java b/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java index d71862eee..7fd9e8671 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java @@ -22,10 +22,13 @@ import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.MutatingApiAction; import org.labkey.api.action.SpringActionController; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.ContainerManager; import org.labkey.api.data.ContainerType; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.RequiresPermission; +import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.permissions.UpdatePermission; import org.labkey.api.util.Pair; import org.springframework.validation.BindException; @@ -64,7 +67,7 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors) return null; } - if (!protocol.getContainer().getContainerFor(ContainerType.DataType.tabParent).equals(getContainer().getContainerFor(ContainerType.DataType.tabParent))) + if (!new ContainerFilter.CurrentAndSubfoldersPlusShared(getContainer().getContainerFor(ContainerType.DataType.tabParent), getUser()).generateIds(getContainer().getContainerFor(ContainerType.DataType.tabParent), ReadPermission.class, getViewContext().getContextualRoles()).contains(protocol.getContainer().getEntityId())) { errors.reject(ERROR_MSG, "Protocol is from the wrong container: " + form.getProtocolId()); logger.error("CacheAnalysesAction targeted a protocol from the wrong container: {}, from {}, in the container: {}", form.getProtocolId(), protocol.getContainer().getPath(), getContainer().getPath()); @@ -151,7 +154,7 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors) return null; } - if (!protocol.getContainer().getContainerFor(ContainerType.DataType.tabParent).equals(getContainer().getContainerFor(ContainerType.DataType.tabParent))) + if (!new ContainerFilter.CurrentAndSubfoldersPlusShared(getContainer().getContainerFor(ContainerType.DataType.tabParent), getUser()).generateIds(getContainer().getContainerFor(ContainerType.DataType.tabParent), ReadPermission.class, getViewContext().getContextualRoles()).contains(protocol.getContainer().getEntityId())) { errors.reject(ERROR_MSG, "Protocol is from the wrong container: " + form.getProtocolId()); logger.error("CacheHaplotypesAction targeted a protocol from the wrong container: {}, from {}, in the container: {}", form.getProtocolId(), protocol.getContainer().getPath(), getContainer().getPath()); diff --git a/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java b/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java index 0af4d376e..04acacdf8 100644 --- a/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java +++ b/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java @@ -22,6 +22,7 @@ import org.junit.BeforeClass; import org.junit.Test; import org.junit.experimental.categories.Category; +import org.labkey.api.util.FileUtil; import org.labkey.remoteapi.query.SelectRowsCommand; import org.labkey.remoteapi.query.TruncateTableCommand; import org.labkey.serverapi.reader.Readers; @@ -62,13 +63,13 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException @BeforeClass public static void setupProject() throws Exception { - PMRTest init = (PMRTest)getCurrentTest(); + PMRTest init = getCurrentTest(); init.doSetup(); } private File getKinshipPath() { - return new File(TestFileUtils.getDefaultFileRoot(getProjectName()), "kinshipEtlDir"); + return FileUtil.appendName(TestFileUtils.getDefaultFileRoot(getProjectName()), "kinshipEtlDir"); } private void doSetup() @@ -143,7 +144,7 @@ private void testKinshipEtl() throws Exception // Verify data imported, and then delete from the DB SelectRowsCommand select1 = new SelectRowsCommand("ehr", "kinship"); - Assert.assertEquals("Incorrect number of kinship rows", 136, select1.execute(getApiHelper().getConnection(), getProjectName()).getRowCount().intValue()); + Assert.assertEquals("Incorrect number of kinship rows", 104, select1.execute(getApiHelper().getConnection(), getProjectName()).getRowCount().intValue()); new TruncateTableCommand("ehr", "kinship").execute(getApiHelper().getConnection(), getProjectName()); Assert.assertEquals("Incorrect number of kinship rows", 0, select1.execute(getApiHelper().getConnection(), getProjectName()).getRowCount().intValue()); @@ -153,7 +154,7 @@ private void testKinshipEtl() throws Exception goToDataPipeline(); waitForPipelineJobsToComplete(4, "ETL Job: Import PRIMe-seq Kinship Data", false); - Assert.assertEquals("Incorrect number of kinship rows after ETL", 136, select1.execute(getApiHelper().getConnection(), getProjectName()).getRowCount().intValue()); + Assert.assertEquals("Incorrect number of kinship rows after ETL", 104, select1.execute(getApiHelper().getConnection(), getProjectName()).getRowCount().intValue()); } private void createTestPedigreeData() throws Exception diff --git a/SivStudies/resources/etls/siv-studies.xml b/SivStudies/resources/etls/siv-studies.xml index c99ffd985..fbd6bcf7e 100644 --- a/SivStudies/resources/etls/siv-studies.xml +++ b/SivStudies/resources/etls/siv-studies.xml @@ -57,7 +57,7 @@ - + diff --git a/SivStudies/resources/queries/study/genetics.query.xml b/SivStudies/resources/queries/study/genetics.query.xml index 334a603e5..07774ea71 100644 --- a/SivStudies/resources/queries/study/genetics.query.xml +++ b/SivStudies/resources/queries/study/genetics.query.xml @@ -14,6 +14,9 @@ Assay Type + + Library Type + Marker/Allele diff --git a/SivStudies/resources/referenceStudy/study/datasets/datasets_metadata.xml b/SivStudies/resources/referenceStudy/study/datasets/datasets_metadata.xml index 2aaf20eac..77f3b4d04 100644 --- a/SivStudies/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/SivStudies/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -427,6 +427,9 @@ varchar + + varchar + varchar diff --git a/mGAP/resources/views/welcome.html b/mGAP/resources/views/welcome.html index 9c330098b..d5cf5fb9b 100644 --- a/mGAP/resources/views/welcome.html +++ b/mGAP/resources/views/welcome.html @@ -14,6 +14,16 @@ } }); }(jQuery, LABKEY)); + + $(document).ready(function () { + $('#slideshow').cycle({ + fx: 'fade', + pager: '#smallnav', + pause: 1, + speed: 1800, + timeout: 3500 + }); + });
@@ -22,85 +32,53 @@
- -