Add models based on the data model

For:
#30

src/hci/models.py

@@ -1,11 +1,124 @@
 """Models of the data in the HCI."""
 
 # Third-party dependencies:
+from django.contrib.auth.models import User
 from django.db import models
 
 
+class Disease(models.Model):
+    """Define the shape of a disease."""
+    mondo_id: models.CharField = models.CharField()
+
+
+class Allele(models.Model):
+    """Define the shape of an allele."""
+    imgt_name: models.CharField = models.CharField()
+    car_id: models.CharField = models.CharField()
+
+
+class Haplotype(models.Model):
+    """Define the shape of a haplotype."""
+    chromosome_mapping_order: models.CharField = models.CharField()
+    constituent_alleles: models.ManyToManyField = models.ManyToManyField(Allele, on_delete=models.PROTECT)
+
+
+class Publication(models.Model):
+    """Define the shape of a publication."""
+    publication_id: models.CharField = models.CharField()
+    publication_type: models.CharField = models.CharField()
+    author: models.CharField = models.CharField()
+    year: models.CharField = models.CharField()
+    title: models.CharField = models.CharField()
+
+
+class Curator(models.Model):
+    """Define the shape of curator."""
+    affiliation_id: models.IntegerField = models.IntegerField()
+    affiliation_name: models.CharField = models.CharField()
+    user: models.OneToOneField = models.OneToOneField(User, on_delete=models.CASCADE)
+
+
+class Association(models.Model):
+    """Define the shape of an association."""
+
+    # Study info:
+    study_type: models.CharField = models.CharField()
+    cohort_type: models.CharField = models.CharField()
+    label: models.CharField = models.CharField()
+
+    allele_field_resolution: models.CharField = models.CharField()
+    is_haplotype: models.BooleanField = models.BooleanField()
+    zygosity: models.CharField = models.CharField()
+
+    # Allele identification methods:
+    allele_name_in_publication: models.CharField = models.CharField()
+    serological: models.BooleanField = models.BooleanField()
+    imputation: models.BooleanField = models.BooleanField()
+    array_data: models.BooleanField = models.BooleanField()
+    low_resolution_typing_ssop: models.BooleanField = models.BooleanField()
+    sanger_sequencing: models.BooleanField = models.BooleanField()
+    whole_exome_sequencing: models.BooleanField = models.BooleanField()
+    whole_genome_sequencing: models.BooleanField = models.BooleanField()
+    high_resolution_typing: models.BooleanField = models.BooleanField()
+    other: models.BooleanField = models.BooleanField()
+    unknown: models.BooleanField = models.BooleanField()
+    reference_panel: models.TextField = models.TextField()
+    typing_methods_description: models.TextField = models.TextField()
+
+    # Demographic info (phenotypes):
+    phenotypes_in_common: models.CharField = models.CharField()
+    common_free_text: models.TextField = models.TextField()
+    not_phenotypes: models.CharField = models.CharField()
+    not_phenotypes_free_text: models.TextField = models.TextField()
+    age_range_type: models.CharField = models.CharField()
+    age_range_value_from: models.PositiveIntegerField = models.PositiveIntegerField()
+    age_range_value_to: models.PositiveIntegerField = models.PositiveIntegerField()
+    age_range_unit: models.CharField = models.CharField()
+
+    # Demographic info (ancestry):
+    reported_ancestry: models.CharField = models.CharField()
+    biogeographical_category: models.CharField = models.CharField()
+    country_or_countries: models.CharField = models.CharField()
+    num_males: models.PositiveIntegerField = models.PositiveIntegerField()
+    num_females: models.PositiveIntegerField = models.PositiveIntegerField()
+
+    # Statistics (power):
+    num_cases_with_variant: models.PositiveIntegerField = models.PositiveIntegerField()
+    num_cases_genotyped_or_sequenced: models.PositiveIntegerField = models.PositiveIntegerField()
+    case_frequency: models.CharField = models.CharField()
+    num_controls_with_variant: models.PositiveIntegerField = models.PositiveIntegerField()
+    num_controls_genotyped_or_sequenced: models.PositiveIntegerField = models.PositiveIntegerField()
+    control_frequency: models.CharField = models.CharField()
+    total_cohort_size: models.PositiveIntegerField = models.PositiveIntegerField()
+
+    # Statistics (value):
+    test_statistic: models.CharField = models.CharField()
+    value: models.IntegerField = models.IntegerField()
+    confidence_interval_from: models.IntegerField()
+    confidence_interval_to: models.IntegerField()
+    standard_error: models.DecimalField = models.DecimalField()
+
+    # Statistics (significance):
+    p_value: models.DecimalField = models.CharField()
+    p_value_type: models.CharField = models.CharField()
+    is_conditional: models.BooleanField = models.BooleanField()
+    condition_on: models.TextField = models.TextField()
+
+    direction_of_effect: models.CharField = models.CharField()
+    comments: models.TextField = models.TextField()
+    score: models.DecimalField = models.DecimalField()
+
+
+class Classification(models.Model):
+    """Define the shape of a classification."""
+    publication: models.ForeignKey = models.ForeignKey(Publication, on_delete=models.PROTECT)
+    curator: models.ForeignKey = models.ForeignKey(Curator, on_delete=models.PROTECT)
+    association: models.ManyToManyField = models.ManyToManyField(Association, on_delete=models.PROTECT)
+
+
 class Curation(models.Model):
     """Define the shape of an HLA curation."""
-
-    disease: models.CharField = models.CharField()
-    hla_allele: models.CharField = models.CharField()
+    disease: models.ForeignKey = models.ForeignKey(Disease, on_delete=models.PROTECT)
+    allele: models.ForeignKey = models.ForeignKey(Allele, on_delete=models.PROTECT)
+    haplotype: models.ForeignKey = models.ForeignKey(Haplotype, on_delete=models.PROTECT)
+    classifications: models.ManyToManyField = models.ManyToManyField(Classification, on_delete=models.PROTECT)