Django and Ensembl - part III

Basic object manipulation. Once the models have validated, we can use the interactive shell (IPython accessed via "python manage.py shell") to play around with data access.

In [1]: from djensembl.djpyensembl.models import CoordSystem

In [2]: CoordSystem.objects.all()

Out[2]: [, , , , ]

5 objects are returned from that call, corresponding to the 5 coord_systems. Just like in the tutorial, that naming system is not very informative. So, I modified the CoordSystem model just like they did by adding the __unicode__ method as such:

def __unicode__(self):
return str(self.coord_system_id) + ' -> ' + self.name

Now I get this:

In [1]: from djensembl.djpyensembl.models import CoordSystem

In [2]: CoordSystem.objects.all()

Out[2]: [ chromosome>, supercontig>, contig>, clone>, chromosome>]

I doubt that's ultimately what I want but it works for now.

Some of the built-in generic behaviors don't work well with this db due to the particular use/misuse/nonuse of the 'id' column. In a Django-centric-developed app, you could issue statements like:

c = CoordSystem.objects.get(pk=1)

But, since the table doesn't have an id column which is the primary key, auto-incremented, this call fails, as does c = CoordSystem.objects.get(id=1), obviously.

What does work is c = CoordSystem.objects.get(coord_system_id=17). I presume this is one of the 'drawback' of using legacy db's where the table structure is not designed with Django's shortcuts in mind. No problemo.