I have an upsert statement that is creating duplicates of Opportunity Line Items instead of updating them. I probably have not got the id in the set I'm upserting but I've looked and can't see how.

Basically, I have a Add Product Page (thanks michaelforce.org for providing the base code) that has everything on one page. 

The apex controller creates a list (shoppingCart) of the existing opportunity line items, as follows:

public opportunityLineItem[] shoppingCart {get;set;}

shoppingCart = [select Id, Quantity, UnitPrice, Budget__c, FlightEnd__c, CampaignName__c,
        SpecialTerms__c, Targeting__c, PricingModel__c, DailyCap__c, Pacing__c, ServiceDate, Description, PriceBookEntryId,
        PriceBookEntry.Name, PriceBookEntry.IsActive, PriceBookEntry.Product2Id, PriceBookEntry.Product2.Name,
        PriceBookEntry.PriceBook2Id from opportunityLineItem where OpportunityId=:theOpp.Id];
//note: I have queried the opp prior to this...

The save function (which is duplicating every line item) is:
// method to delete any removed lines and add/update selected rows
    public PageReference onSave(){
        Savepoint sp = Database.setSavepoint();
        try{
            // If previously selected products are now removed, we need to delete them
            if(forDeletion.size()>0)
                delete(forDeletion);
       
            // Previously selected products may have new quantities and amounts, and we may have new products listed, so we use upsert here
            // if we have products, upsert them
            if(shoppingCart.size()>0) {
                // grab all OLIs and upsert them
                List<OpportunityLineItem> olis = new List<OpportunityLineItem>();
                for (OpportunityLineItem oli : shoppingCart) olis.add(oli);
                upsert olis;
            }
        }
        catch(Exception e){
            Database.rollback(sp);         
            ApexPages.addMessages(e);
            return null;
        }

So, it seems like ID isn't getting added to the olis list? I tried upsert olis id; just for kicks but then got an error "field integrity exception: unknown (scheduling not enabled on product)". Then for fun, I tried update olis; and got the issue "id not specified in an update call". But didn't I specify the ids in the initial query for ShoppingCart (i.e. [select Id from OpportunityLineItem where...])

I also tried to create the shopping cart list a little differently:

(for OpportunityLineItem oli : [select Id, Quantity, UnitPrice, Budget__c, FlightEnd__c, CampaignName__c,
        SpecialTerms__c, Targeting__c, PricingModel__c, DailyCap__c, Pacing__c, ServiceDate, Description, PriceBookEntryId,
        PriceBookEntry.Name, PriceBookEntry.IsActive, PriceBookEntry.Product2Id, PriceBookEntry.Product2.Name,
        PriceBookEntry.PriceBook2Id from opportunityLineItem where OpportunityId=:theOpp.Id]){
shoppingcart.add(oli) }

but then get an attempt to dereference a null object error when I open the page. 

I ran this code and added system debugs and it's finding the opp but my system debug message that comes right after assigning to the shopping cart never does appear.