Failed to create annotation file /space/gemmaData/microAnnots/GPL6105_bioProcess.an.txt.gz for ArrayDesign Id=347 Name=Illumina mouse-6 v1.1 expression beadchips (GPL6105).

[arteymix]

There's ACL issues for that platform:

IllegalStateException: ACLs did not contain key for parent object identity of gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 1972]( parent = gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperiment; Identifier: 1567]); ACLs being inspected: AclImpl[id: 229921; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis; Identifier: 4066]; owner: AclPrincipalSid[administrator]; no ACEs; inheriting: true; parent: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 1967]; aclAuthorizationStrategy: gemma.gsec.acl.AclAuthorizationStrategyImpl@2cd6773b; ] AclImpl[id: 229927; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 1969]; owner: AclPrincipalSid[administrator]; AclEntry[id: 305877; granting: true; sid: AclGrantedAuthoritySid[GROUP_ADMIN]; permission: BasePermission[...........................A....=16]; ] AclEntry[id: 305878; granting: true; sid: AclGrantedAuthoritySid[GROUP_AGENT]; permission: BasePermission[...............................R=1]; ] AclEntry[id: 305879; granting: true; sid: AclGrantedAuthoritySid[IS_AUTHENTICATED_ANONYMOUSLY]; permission: BasePermission[...............................R=1]; ] inheriting: true; parent: Null; aclAuthorizationStrategy: gemma.gsec.acl.AclAuthorizationStrategyImpl@2cd6773b; ] AclImpl[id: 229931; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 1970]; owner: AclPrincipalSid[administrator]; AclEntry[id: 305886; granting: true; sid: AclGrantedAuthoritySid[GROUP_ADMIN]; permission: BasePermission[...........................A....=16]; ] AclEntry[id: 305887; granting: true; sid… java.lang.IllegalStateException: ACLs did not contain key for parent object identity of gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 1972]( parent = gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperiment; Identifier: 1567]); ACLs being inspected: AclImpl[id: 229921; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis; Identifier: 4066]; owner: AclPrincipalSid[administrator]; no ACEs; inheriting: true; parent: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression…

[arteymix]

It happened while generating annotation file for GPL6480 too:

ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl.downloadAnnotationFile(215) | Failed to create annotation file /space/gemmaData/microAnnots/GPL6480_bioProcess.an.txt.gz for ArrayDesign Id=420 Name=Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) (GPL6480).

This is caused by some ACL issues for an EE subset.

AclImpl[id: 860287; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis; Identifier: 31373]; owner: AclPrincipalSid[jchoi]; no ACEs; inheriting: true; parent: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 6029]; aclAuthorizationStrategy: gemma.gsec.acl.AclAuthorizationStrategyImpl@521eb304; ]
AclImpl[id: 860286; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 6029]; owner: AclPrincipalSid[jchoi]; no ACEs; inheriting: true; parent: Null; aclAuthorizationStrategy: gemma.gsec.acl.AclAuthorizationStrategyImpl@521eb304; ]
AclImpl[id: 860283; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 6028]; owner: AclPrincipalSid[jchoi]; no ACEs; inheriting: true; parent: Null; aclAuthorizationStrategy: gemma.gsec.acl.AclAuthorizationStrategyImpl@521eb304; ]
java.lang.IllegalStateException: ACLs did not contain key for parent object identity of gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; Identifier: 6029]( parent = gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experiment.ExpressionExperiment; Identifier: 6027]); ACLs being inspected: AclImpl[id: 860284; objectIdentity: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis; Identifier: 31372]; owner: AclPrincipalSid[jchoi]; no ACEs; inheriting: true; parent: gemma.gsec.acl.domain.AclObjectIdentity[Type: ubic.gemma.model.expression.experi…```

[arteymix]

There is a potential fix for this in https://github.com/PavlidisLab/gsec/pull/27. This is likely caused by a long-standing bug in how parent ACL identities are being retrieved.

Fix would be in b2690f5957d710e78aaf8317c8b0c922ba79c1bf.