Examples with AuditTrailService ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService used on opensource projects

Example 1 with AuditTrailService

use of ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService in project Gemma by PavlidisLab.

the class ExpressionExperimentDataFileGeneratorCli method processExperiment.

private void processExperiment(ExpressionExperiment ee) {
    try {
        ee = this.eeService.thawLite(ee);
        AuditTrailService ats = this.getBean(AuditTrailService.class);
        AuditEventType type = CommentedEvent.Factory.newInstance();
        expressionDataFileService.writeOrLocateCoexpressionDataFile(ee, force_write);
        expressionDataFileService.writeOrLocateDiffExpressionDataFiles(ee, force_write);
        ats.addUpdateEvent(ee, type, "Generated Flat data files for downloading");
        super.successObjects.add("Success:  generated data file for " + ee.getShortName() + " ID=" + ee.getId());
    } catch (Exception e) {
        AbstractCLI.log.error(e, e);
        super.errorObjects.add("FAILED: for ee: " + ee.getShortName() + " ID= " + ee.getId() + " Error: " + e.getMessage());
    }
}

Example 2 with AuditTrailService

use of ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService in project Gemma by PavlidisLab.

the class ExpressionExperimentPlatformSwitchCli method processExperiment.

private void processExperiment(ExpressionExperiment ee) {
    try {
        ee = this.eeService.thawLite(ee);
        AuditTrailService ats = this.getBean(AuditTrailService.class);
        AuditEventType type = ExpressionExperimentPlatformSwitchEvent.Factory.newInstance();
        if (this.arrayDesignName != null) {
            ArrayDesign ad = this.locateArrayDesign(this.arrayDesignName, arrayDesignService);
            if (ad == null) {
                AbstractCLI.log.error("Unknown array design");
                this.bail(ErrorCode.INVALID_OPTION);
            }
            ad = arrayDesignService.thaw(ad);
            ee = serv.switchExperimentToArrayDesign(ee, ad);
            ats.addUpdateEvent(ee, type, "Switched to use " + ad);
        } else {
            // Identify merged platform automatically; not really recommended as it might not make the optimal choice.
            ee = serv.switchExperimentToMergedPlatform(ee);
            ats.addUpdateEvent(ee, type, "Switched to use merged array Design ");
        }
        super.successObjects.add(ee.toString());
    } catch (Exception e) {
        AbstractCLI.log.error(e, e);
        super.errorObjects.add(ee + ": " + e.getMessage());
    }
}