Correct way to delete a field, add a field and update attributes in pyqgis

Question

I am working on a script that runs a model and then appends the result to a spatialite layer. The model runs zonal statistics using 4 different rasters and appends them to the attribute table of a vector polygon layer with a single feature. The attribute table of the model output (habitatModel) looks as follows:

id  | hs90_mean | hs14_mean | ls90_mean | ls14_mean
----+-----------+-----------+-----------+----------
 1  | 46.043816 | 44.009554 | 47.859847 | 45.308090

The type of the id field is integer, and I need to replace that with a string identifier, so I load the layer as a QgsVectorLayer, add a genspec field and delete the id field:

habitatModelLayer = QgsVectorLayer(habitatModel,genspec,'ogr')
habitatModelLayer.dataProvider().addAttributes([QgsField("genspec", QVariant.String)])
habitatModelLayer.dataProvider().deleteAttributes([habitatModelLayer.fields().lookupField('id')])
habitatModelLayer.updateFields()

Then I try to update the attribute values using dataprovider().changeAttributeValues():

iterator = habitatModelLayer.getFeatures(QgsFeatureRequest().setFilterFid(0))
feature = next(iterator)
attrs = {habitatModelLayer.fields().lookupField('genspec'):'2759-9',
    habitatModelLayer.fields().lookupField('hs90_mean'):feature['hs90_mean'],
    habitatModelLayer.fields().lookupField('ls90_mean'):feature['ls90_mean'],
    habitatModelLayer.fields().lookupField('hs14_mean'):feature['hs14_mean'],
    habitatModelLayer.fields().lookupField('ls14_mean'):feature['ls14_mean']}
habitatModelLayer.dataProvider().changeAttributeValues({0:attrs})
habitatModelLayer.commitChanges()

I then add the layer to the spatialite file database using qgis:importintospatialite:

processing.run("qgis:importintospatialite", {
    'INPUT':habitatModelLayer,
    'DATABASE':spatialiteLayer,
    'TABLENAME':'models',
    'PRIMARY_KEY':'genspec',
    'GEOMETRY_COLUMN':'geom',
    'ENCODING':'UTF-8',
    'OVERWRITE':True,
    'CREATEINDEX':True,
    'LOWERCASE_NAMES':False,
    'DROP_STRING_LENGTH':False,
    'FORCE_SINGLEPART':False
})

The resulting layer has the correct values for the zonal stats, but the genspec field is empty. Any idea why this would be?

A strange side-note is that when the habitatModel layer is added to the canvas as a result of the script, it initially still shows the new attributes squashed into the old fields (and trying to conform to the old types):

id  | hs90_mean | hs14_mean | ls90_mean | ls14_mean
----+-----------+-----------+-----------+----------
 46 | 44.009554 | 47.859847 | 45.308090 | 2795

but after a few minutes the attribute table corrects itself:

 hs90_mean | hs14_mean | ls90_mean | ls14_mean | genspec
-----------+-----------+-----------+-----------+---------
 46.043816 | 44.009554 | 47.859847 | 45.308090 | 2759-9

Is there some kind of buffer that needs to be flushed before I write to the spatialite database?

Answer 1

I think there was an issue somehow because the order of the fields changed. I ended up taking a different approach. Since I'm only really interested in the feature, not the layer, I created a copy of the feature and used the dataProvider() for the spatialite layer to add the feature there. The working code is as follows:

    # fetch feature and map attributes for destination layer
    habitatModelLayer = QgsVectorLayer(habitatModel,genspec,'ogr')
    iterator = habitatModelLayer.getFeatures(QgsFeatureRequest().setFilterFid(0))
    feature = next(iterator)
    spatialiteFeature = QgsFeature(feature)        # make a copy        
    spatialiteFields = spatialiteLayer.fields()
    spatialiteFeature.setFields(spatialiteFields)  # replace source with destination fields
    for f in spatialiteFeature.fields().names():
        if f == 'genspec':
            spatialiteFeature[f] = genspec      # in destination but not source layer
        else:
            spatialiteFeature[f] = feature[f]   # map destination to source attributes

    # first delete any existing features with this id (genspec)
    spatialiteLayer.startEditing()              # deleteFeature requires an active edit session
    filter = QgsExpression.createFieldEqualityExpression('genspec',genspec)
    request = QgsFeatureRequest().setFilterExpression(filter)
    request.setSubsetOfAttributes([])
    request.setFlags(QgsFeatureRequest.NoGeometry)
    for f in spatialiteLayer.getFeatures(request):
        feedback.pushInfo(f"Found existing model with genspec {genspec}. Replacing with new model.")
        spatialiteLayer.deleteFeature(f.id())
    spatialiteLayer.commitChanges()

    # add feature to destination layer
    if not spatialiteLayer.dataProvider().addFeatures([spatialiteFeature]):
        feedback.pushError(f"Error adding model for taxon {genspec} to spatialite:") 
        for f in spatialiteFeature.fields().names():
            feedback.pushInfo(f"{f}: {spatialiteFeature.attributes()[spatialiteFeature.fields().lookupField(f)]}")