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I have a django application 'test_app'. The test_app page - "domain/test_app/" has a link to another page within the app "Genes". This takes me to "domain/test_app/genes/". In this page I have a list of links which comes from my a table in my django database called "gene", which is in test_app/models.py as class Gene. This links to another table called "Variants" via attribute 'gene' as a foreign key.

This is all in test_app/models.py:

class Gene(models.Model):
    gene = models.CharField(primary_key=True, max_length=110)
    transcript = models.CharField(max_length=100)

    def __str__(self):
        return self.gene


class Variant(models.Model):
    variant = models.CharField(primary_key=True, max_length=210)
    gene = models.ForeignKey(Gene, on_delete=models.CASCADE)
    cds = models.CharField(max_length=150)

    def __str__(self):
        return self.variant

My test_app/urls.py urlpatterns look like this:

urlpatterns = [
    url(r'^$', views.test_app, name='test_app'),
    url(r'^genes/$', views.genes, name='genes'),
    url(r'^genes/(?P<gene>)', views.variant_info, name='variant_info'),
]

and test_app/views.py look like this (link to test_app/templates/test_app/ directory with my templates in):

def test_app(request):
    template = loader.get_template('test_app/index.html')
    return render(request, 'test_app/index.html')

def genes(request):
    gene_list = Gene.objects.all()
    context = {'gene_list': gene_list}
    return render(request, 'test_app/genes.html', context)

def variant_info(request, gene):
    variant_info = Variant.objects.filter(gene=gene)
    return(request, 'test_app/gene_info.html', {'variant_info': variant_info}

I have a list of genes in my gene table in my database. When obtaining these genes using 'gene_list = Gene.objects.all()' this works fine. I then render this list to a template as a series of links on my "domain/test_app/genes" page. For example, when I click on TP53 on this page, it goes to "domain/test_app/genes/TP53/". This takes me to the correct page.

However, I clearly do not have the regex for this urlpattern correct as when I type in more digits or characters such as /TP53098120918 it still goes to the same page. Even when I put r'^genes/(?P)$' this is still happening and I dont understand why?

But the main problem I am having is obtaining the information from my variant table in my database and rendering this to the specific gene page, such as domain/test_app/genes/TP53.

When I am clicking on the TP53 it does not pass through to my view function 'variant_info' as the gene argument because the line:

variant_info = Variant.objects.filter(gene=gene)

does not obtain any information from the database - i thought this would pass gene='TP53' when I click on the link, and therefore this would be:

variant_info = Variant.objects.filter(gene='TP53')

which would return the information from the variant table with the gene as TP53. I don't know how to properly access the TP53 from the genes function in views.py.

trouselife
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  • In urls.py you should include the regular expression correctly, for example if you want to get genes by id: `url(r'^genes/(?P\d+)', views.variant_info, name='variant_info'),` this way the gene id is passed to the view, then you should retrieve variant objects this way: `variant_info = Variant.objects.filter(gene__id=gene)` – abidibo Nov 08 '16 at 16:27
  • I don't have gene ids in my table. The primary key is the gene name – trouselife Nov 08 '16 at 16:32
  • oh, I see. That's quite uncommon, either way, define the characters to match in the reg exp: `url(r'^genes/(?P[^/]+)', views.variant_info, name='variant_info')` and then `variant_info = Variant.objects.filter(gene__gene=gene)` – abidibo Nov 08 '16 at 16:35
  • The genes do not have ids though - the gene table has gene attribute which is the primary key - not an incremental id. because I have a large database that I will end up incorporating which doesnt use unique digit ids. So I am trying to query the Variant table using my gene name (which is a foreign key in variant table) to access the information, and render this to my test_app/genes/TP53 page. However when I click on the TP53 it obviously isnt getting inherited into the variant_info function as the variant_info variable is null when using "variant_info = Variant.objects.filter(gene=gene) – trouselife Nov 08 '16 at 16:44

2 Answers2

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The problem is that your (?P<gene>) is not matching any characters, so you will always have gene='' in your view.

Try changing your url pattern to:

url(r'^genes/(?P<gene>\w+)/$', views.variant_info, name='variant_info'),

This will accept letters A-Z, a-z, digits 0-9 and underscore for the gene argument. I've added the trailing slash for consistency with your other views, and the dollar because it's usually a good idea to do this.

Alasdair
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for the url you'd need something like to match only digits at the end

r'^genes/(?P<gene>TP\d+)$'

(I think otherwise it will try to match a string and just accept the first match)

as for your second question: sorry, but I don't get what you're asking. But looking at your code I assume you want to filter by properties of the foreign Model:

variant_info = Variant.objects.filter(gene__gene__contains=gene)

This means to search in field gene of object Gene.

ps. that starts to look confusing, I would suggest changing the model to something like

class Gene(models.Model): 
  name = models.CharField(primary_key=True, max_length=110)
  ...
Alex
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  • What I want is when I click on TP53 this string ("TP53") is passed through my urls regex r'^genes/(?P)' as so that this is inherited in my view.py function "variant_info" so that on the test_app/genes/TP53 page it will query the Variant table in my database using the argument gene="TP53" and I can render the query results to this page. – trouselife Nov 08 '16 at 16:46