More logging to diagnose why beam locations are not saved correctly f…

…or uploaded datasets. Fixed some error handling too

api/dataimport/internal/output/output.go

@@ -318,6 +318,10 @@ func (s *PIXLISEDataSaver) Save(
 
 	// We work out the default file name when copying output images now... because if there isn't one, we may pick one during that process.
 	defaultContextImage, err := copyImagesToOutput(contextImageSrcPath, []string{data.DatasetID}, data.DatasetID, outputImagesPath, data, db, jobLog)
+	if err != nil {
+		return err
+	}
+
 	exp.MainContextImage = defaultContextImage
 
 	// Set any matched aligned images - this happens after copyImagesToOutput because file names may be modified by it depending on formats
@@ -359,7 +363,7 @@ func (s *PIXLISEDataSaver) Save(
 
 	summaryData := makeSummaryFileContent(&exp, data.DatasetID, data.Instrument, data.Meta, int(fi.Size()), creationUnixTimeSec, data.CreatorUserId)
 
-	jobLog.Infof("Writing summary to DB...")
+	jobLog.Infof("Writing summary to DB for %v...", summaryData.Id)
 
 	coll = db.Collection(dbCollections.ScansName)
 	opt := options.Update().SetUpsert(true)
@@ -374,14 +378,15 @@ func (s *PIXLISEDataSaver) Save(
 	}
 
 	// Set ownership
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(summaryData.Id, protos.ObjectType_OT_SCAN, summaryData.CreatorUserId, creationUnixTimeSec)
+	ownerItem := wsHelpers.MakeOwnerForWrite(summaryData.Id, protos.ObjectType_OT_SCAN, summaryData.CreatorUserId, creationUnixTimeSec)
 
 	ownerItem.Viewers = autoShare.Viewers
 	ownerItem.Editors = autoShare.Editors
 
 	coll = db.Collection(dbCollections.OwnershipName)
 	opt = options.Update().SetUpsert(true)
 
+	jobLog.Infof("Writing ownership to DB for scan %v...", ownerItem.Id)
 	result, err = coll.UpdateOne(context.TODO(), bson.D{{Key: "_id", Value: ownerItem.Id}}, bson.D{{Key: "$set", Value: ownerItem}}, opt)
 	if err != nil {
 		jobLog.Errorf("Failed to write ownership item to DB: %v", err)
@@ -408,10 +413,13 @@ func insertDefaultImage(db *mongo.Database, scanId string, defaultImage string,
 	coll := db.Collection(dbCollections.ScanDefaultImagesName)
 	opt := options.InsertOne()
 
-	defaultImageResult, err := coll.InsertOne(context.TODO(), &protos.ScanImageDefaultDB{ScanId: scanId, DefaultImageFileName: path.Join(scanId, defaultImage)}, opt)
+	imgPath := path.Join(scanId, defaultImage)
+	jobLog.Infof("Writing default image %v to DB for scan %v...", imgPath, scanId)
+	defaultImageResult, err := coll.InsertOne(context.TODO(), &protos.ScanImageDefaultDB{ScanId: scanId, DefaultImageFileName: imgPath}, opt)
 	if err != nil {
 		if mongo.IsDuplicateKeyError(err) {
 			// Don't overwrite, so we're OK with this
+			jobLog.Infof("Default image for scan %v already exists, not overwriting existing one in case of user edit.", scanId)
 			return nil
 		}
 		return err

api/quantification/create.go

@@ -382,12 +382,7 @@ func (r *quantNodeRunner) triggerPiquantNodes(wg *sync.WaitGroup) {
 		},
 	}
 
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(r.jobId, protos.ObjectType_OT_QUANTIFICATION, r.quantStartSettings.RequestorUserId, now)
-	if err != nil {
-		msg := fmt.Sprintf("Failed to create ownership info for quant job %v. Error was: %v", r.jobId, err)
-		r.completeJobState(false, msg, quantOutPath, piquantLogList)
-		return
-	}
+	ownerItem := wsHelpers.MakeOwnerForWrite(r.jobId, protos.ObjectType_OT_QUANTIFICATION, r.quantStartSettings.RequestorUserId, now)
 
 	err = writeQuantAndOwnershipToDB(summary, ownerItem, svcs.MongoDB)
 	if err != nil {

api/quantification/importCSV.go

@@ -66,10 +66,7 @@ func ImportQuantCSV(
 	}
 
 	// Finally, write the summary data to DB along with ownership entry
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(quantId, protos.ObjectType_OT_QUANTIFICATION, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
-	if err != nil {
-		return quantId, err
-	}
+	ownerItem := wsHelpers.MakeOwnerForWrite(quantId, protos.ObjectType_OT_QUANTIFICATION, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
 
 	summary := protos.QuantificationSummary{
 		Id:     quantId,

api/ws/handlers/element-set.go

@@ -101,10 +101,8 @@ func createElementSet(elementSet *protos.ElementSet, hctx wsHelpers.HandlerConte
 	elementSet.Id = id
 
 	// We need to create an ownership item along with it
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_ELEMENT_SET, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
-	if err != nil {
-		return nil, err
-	}
+	ownerItem := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_ELEMENT_SET, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
+
 	elementSet.ModifiedUnixSec = ownerItem.CreatedUnixSec
 
 	wc := writeconcern.New(writeconcern.WMajority())

api/ws/handlers/expression-group.go

@@ -106,10 +106,7 @@ func createExpressionGroup(egroup *protos.ExpressionGroup, hctx wsHelpers.Handle
 	egroup.Id = id
 
 	// We need to create an ownership item along with it
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_EXPRESSION_GROUP, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
-	if err != nil {
-		return nil, err
-	}
+	ownerItem := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_EXPRESSION_GROUP, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
 
 	egroup.ModifiedUnixSec = ownerItem.CreatedUnixSec
 

api/ws/handlers/expression.go

@@ -110,10 +110,7 @@ func createExpression(expr *protos.DataExpression, hctx wsHelpers.HandlerContext
 	expr.Id = id
 
 	// We need to create an ownership item along with it
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_EXPRESSION, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
-	if err != nil {
-		return nil, err
-	}
+	ownerItem := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_EXPRESSION, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
 
 	expr.ModifiedUnixSec = ownerItem.CreatedUnixSec
 

api/ws/handlers/module.go

@@ -262,10 +262,7 @@ func createModule(name string, comments string, intialSourceCode string, tags []
 	}
 
 	// We need to create an ownership item along with it
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(modId, protos.ObjectType_OT_DATA_MODULE, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
-	if err != nil {
-		return nil, err
-	}
+	ownerItem := wsHelpers.MakeOwnerForWrite(modId, protos.ObjectType_OT_DATA_MODULE, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
 
 	module.ModifiedUnixSec = ownerItem.CreatedUnixSec
 

api/ws/handlers/roi.go

@@ -180,10 +180,7 @@ func createROI(roi *protos.ROIItem, hctx wsHelpers.HandlerContext, needMistEntry
 	roi.Id = id
 
 	// We need to create an ownership item along with it
-	ownerItem, err := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_ROI, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
-	if err != nil {
-		return nil, err
-	}
+	ownerItem := wsHelpers.MakeOwnerForWrite(id, protos.ObjectType_OT_ROI, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
 
 	roi.ModifiedUnixSec = ownerItem.CreatedUnixSec
 

api/ws/handlers/screen-configuration.go

@@ -156,10 +156,7 @@ func writeScreenConfiguration(screenConfig *protos.ScreenConfiguration, hctx wsH
 			}
 
 			// We need to create an ownership item along with it
-			owner, err = wsHelpers.MakeOwnerForWrite(screenConfig.Id, protos.ObjectType_OT_SCREEN_CONFIG, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
-			if err != nil {
-				return nil, err
-			}
+			owner = wsHelpers.MakeOwnerForWrite(screenConfig.Id, protos.ObjectType_OT_SCREEN_CONFIG, hctx.SessUser.User.Id, hctx.Svcs.TimeStamper.GetTimeNowSec())
 
 			screenConfig.ModifiedUnixSec = owner.CreatedUnixSec
 			configuration = screenConfig

api/ws/wsHelpers/ownership.go

@@ -15,7 +15,7 @@ import (
 	"go.mongodb.org/mongo-driver/mongo/options"
 )
 
-func MakeOwnerForWrite(objectId string, objectType protos.ObjectType, creatorUserId string, createTimeUnixSec int64) (*protos.OwnershipItem, error) {
+func MakeOwnerForWrite(objectId string, objectType protos.ObjectType, creatorUserId string, createTimeUnixSec int64) *protos.OwnershipItem {
 	ownerItem := &protos.OwnershipItem{
 		Id:             objectId,
 		ObjectType:     objectType,
@@ -30,7 +30,7 @@ func MakeOwnerForWrite(objectId string, objectType protos.ObjectType, creatorUse
 		}
 	}
 
-	return ownerItem, nil
+	return ownerItem
 }
 
 // Checks object access - if requireEdit is true, it checks for edit access

core/beamLocation/experimentFileToDB.go

@@ -47,6 +47,8 @@ func ImportBeamLocationToDB(imgName string, instrument protos.ScanInstrument, fo
 	})
 
 	opt := options.Replace().SetUpsert(true)
+	logger.Infof("Writing beam location to DB for image: %v, and scan: %v, instrument: %v, beamVersion: %v", imgName, forScanId, instrument, beamVersion)
+
 	result, err := imagesColl.ReplaceOne(context.TODO(), bson.M{"_id": imgName}, beams, opt)
 	if err != nil {
 		return err