Application Mutation¶
The MUTATION application contains the actions to generate index mutation from Nextclade.
Key files of the « MUTATION » application¶
management.commands¶
run_index_mutation.py¶
- class apps.mutation.management.commands.run_index_mutation.Command(stdout=None, stderr=None, no_color=False, force_color=False)¶
- handle(*args, **kwargs)¶
SUMMARY LINE
Run task for non index file
HOW TO USE
docker-compose exec web python manage.py run_index_mutation
Add
-f docker-compose.prod.yml
in Prod
models.py¶
- class apps.mutation.models.AlertVariant(*args, **kwargs)¶
Alert variant table
- exception DoesNotExist¶
- exception MultipleObjectsReturned¶
- clean()¶
The clean function checks various fields and performs database checks based on the type of the field.
- class apps.mutation.models.GenomicFeature(*args, **kwargs)¶
Genomic Feature table
- exception DoesNotExist¶
- exception MultipleObjectsReturned¶
- class apps.mutation.models.IntermediateMutationGenomic(id, mutation, result)¶
- exception DoesNotExist¶
- exception MultipleObjectsReturned¶
- class apps.mutation.models.IntermediateMutationProteomic(id, mutation, result)¶
- exception DoesNotExist¶
- exception MultipleObjectsReturned¶
- class apps.mutation.models.MutationGenomic(*args, **kwargs)¶
Mutation nucleotide table
- exception DoesNotExist¶
- exception MultipleObjectsReturned¶
- class apps.mutation.models.MutationProteomic(*args, **kwargs)¶
Mutation proteomic table
- exception DoesNotExist¶
- exception MultipleObjectsReturned¶
- class apps.mutation.models.Protein(*args, **kwargs)¶
Protein table
- exception DoesNotExist¶
- exception MultipleObjectsReturned¶
test.py¶
- class apps.mutation.tests.mutationAlertTestCase(methodName='runTest')¶
Test for alert mutation app
- setUp()¶
Hook method for setting up the test fixture before exercising it.
- tearDown()¶
Hook method for deconstructing the test fixture after testing it.
- test_explore_mutation_log_text()¶
Test get explore page
- class apps.mutation.tests.mutationTaskTestCase(methodName='runTest')¶
Test for mutation task functions
- setUp()¶
Hook method for setting up the test fixture before exercising it.
- tearDown()¶
Hook method for deconstructing the test fixture after testing it.
- test_index_mutation()¶
Test index mutation
- test_index_mutation_auto()¶
Test index mutation auto
- class apps.mutation.tests.mutationTestCase(methodName='runTest')¶
Test for mutation app
- setUp()¶
Hook method for setting up the test fixture before exercising it.
- test_str_Protein()¶
Test model : get str from Protein
- test_str_SeqName()¶
Test model : get str from Seqnam
- test_upload_gene_bad_extension()¶
Test admin upload gene bad extension
- test_upload_gene_bad_file()¶
Test admin upload gene bad file
- test_upload_gene_error()¶
Test admin upload gene error
- test_upload_genomic()¶
Test admin upload genomic feature
- test_upload_proteomic()¶
Test admin upload proteomic feature
- test_upload_proteomic_bad_extension()¶
Test admin upload proteomi bad extension
- test_upload_proteomic_bad_file()¶
Test admin upload proteomic bad file
- test_upload_proteomic_error()¶
Test admin upload proteomic error
views.py¶
- apps.mutation.views.alert_results(request, name=None)¶
The function alert_results retrieves alerts from the database and renders them in a template, with the option to filter by name.
- Paramètres
request – The request parameter is an object that represents the HTTP request made by the client. It contains information such as the request method, headers, and body
name – The name parameter is an optional parameter that represents the name of an alert variant. If provided, the function will try to retrieve the alert variant with the given name from the database. If no alert variant with the given name is found, an error message will be displayed in the rendered template
- Renvoie
The function alert_results returns a rendered HTML template. The specific template being rendered depends on the conditions in the code. If the name parameter is provided and a corresponding AlertVariant object is found, a template with the name “mutation/alert_results.html” is rendered with various variables passed to it. If the name parameter is not provided.
- apps.mutation.views.alert_summary(request)¶
The function « alert_summary » renders a template called « mutation/alert_summary.html » and passes a dictionary containing the names of all fields in the « AlertVariant » model, excluding the primary key field.
- Paramètres
request – The request parameter is an object that represents the HTTP request made by the client. It contains information such as the request method, headers, and body. It is typically passed to view functions in Django to handle the request and generate a response. In this case, it is being passed to the
- Renvoie
a rendered HTML template called “mutation/alert_summary.html” with a context dictionary containing a list of column names from the AlertVariant model.