forms.py

"""
iPPI-DB django forms
"""

from django import forms
from django.core.validators import RegexValidator
from django.forms import ModelForm, modelformset_factory, formset_factory, BaseFormSet

from .models import *
from .ws import pdb_entry_exists

""" Step 1 : IdForm """
class IdFormOld(ModelForm):
    class Meta:
        model = Bibliography
        fields = ['source','id_source']
        labels = {
            "id_source": "ID"
        }
        widgets = {
            'source' : forms.RadioSelect,
            'id_source': forms.TextInput(),
        }


class IdForm(forms.Form):
    source = forms.ChoiceField(
        label='Bibliographic type',
        choices=Bibliography.SOURCES,
        initial='PM',
        widget=forms.RadioSelect,
    )
    id_source = forms.CharField(
        label='Bibliographic ID',
        max_length=25,
    )

    def clean(self):
        ret = super().clean()
        Bibliography.validate_source_id(ret["id_source"], ret["source"])
        return ret

    def get_or_create(self):
        kwargs = dict(source=self.cleaned_data["source"],
                      id_source=self.cleaned_data["id_source"],
                      )
        try:
            b = Bibliography.objects.get(**kwargs)
            return b, False
        except Bibliography.DoesNotExist:
            pass
        b = Bibliography(**kwargs)
        b.save(autofill=True)
        return b, True


""" Step 2 : BibliographyForm """
class BibliographyForm(ModelForm):
    class Meta:
        model = Bibliography
        exclude = ['biblio_year']
        widgets = {
            'source': forms.TextInput(attrs={'readonly':'readonly'}),
            'id_source': forms.TextInput(attrs={'readonly':'readonly'}),
            'title': forms.TextInput(attrs={'readonly':'readonly'}),
            'journal_name': forms.TextInput(attrs={'readonly':'readonly'}),
            'authors_list': forms.TextInput(attrs={'readonly':'readonly'}),
        }


""" Step 3 : PDBForm """
def validate_pdb_exists(value):
    if not(pdb_entry_exists(value)):
        raise ValidationError(
            'PDB entry not found: %(value)s', params={'value': value}, code='invalid')


class PDBForm(forms.Form):
    pdb_id = forms.CharField(
        label="PDB ID",
        max_length=4,
        widget=forms.TextInput(
            attrs={
                'placeholder': 'e.g 3u85',
                'required': 'required',
            }),
        required=True,
        validators=[
            RegexValidator(
                '^[0-9][a-zA-Z0-9]{3}$', message='PDB ID must be 1 numeric + 3 alphanumeric characters'),
            validate_pdb_exists
        ])


class ProteinForm(ModelForm):

    class Meta:
        model = Protein
        exclude = ['recommended_name_long', 'short_name']
        widgets = {
            'uniprot_id': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
            'gene_name': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
            'entry_name': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
            'organism': forms.TextInput(attrs={'readonly': 'readonly', 'class': 'readonly'}),
        }

ProteinFormSet = modelformset_factory(
    Protein, exclude=('recommended_name_long', 'short_name'), extra=0)


""" Step 4 : ProteinDomainComplexTypeForm aka. Architecture """
TYPE_COMPLEX = (
    ('inhibited', 'Inhibited'),
    ('stabilized', 'Stabilized'),
)

TYPE_CHOICES = (
    ('Hetero2merAB', 'Inhib_Hetero 2-mer AB'),
    ('Homo2merA2', 'Inhib_Homo 2-mer A2'),
    ('custom', 'Inhib_Custom'),
    ('Hetero2merAB', 'Stab_Hetero 2-mer AB'),
    ('Homo2merA2', 'Stab_Homo 2-mer A2'),
    ('HomoLike2mer', 'Stab_Homo-Like 2-mer A2'),
    ('Homo3merA3', 'Stab_Homo 3-mer A3'),
    ('Homo3merA2', 'Stab_Homo 3-mer A3 inhibited A2-dimer'),
    ('Homo4merA4', 'Stab_Homo 4-mer A4'),
    ('RingHomo3mer', 'Stab_Ring-Like 3-mer A3'),
    ('RingHomo5mer', 'Stab_Ring-Like 5-mer A5'),
    ('custom', 'Stab_Custom'),
)


class ProteinDomainComplexTypeForm(forms.Form):
    complexChoice=forms.CharField(label="PPI Complex Type", widget=forms.Select(choices=TYPE_COMPLEX))
    complexType=forms.CharField(widget=forms.RadioSelect(choices=TYPE_CHOICES))
    

""" Step 5 : ProteinDomainComplexForm aka. Composition """
class ProteinDomainComplexForm(ModelForm):

    class Meta:
        model=ProteinDomainComplex
        fields=['protein', 'domain', 'ppc_copy_nb']

COMPLEX_TYPE = (
    ('Bound', 'Bound'),
    ('Partner', 'Partner')
)

class ComplexCompositionForm(forms.Form):
    complex_type=forms.CharField(widget=forms.Select(choices=COMPLEX_TYPE, attrs={'class':'form-control', 'onchange':'myFunction()'}))
    complex_protein=forms.ModelChoiceField(queryset=Protein.objects.all(), required=True, widget=forms.Select(attrs={'class':'form-control'}),empty_label=None)
    complex_domain=forms.ModelChoiceField(queryset=Domain.objects.all(), required=True,widget=forms.Select(attrs={'class':'form-control'}),empty_label=None)
    ppc_copy_nb=forms.IntegerField(initial=1,required=True,widget=forms.NumberInput(attrs={'class':'form-control'}))

    def __init__(self,pks=None,*args,**kwargs):
        super(ComplexCompositionForm, self).__init__(*args, **kwargs)
        if pks is not None:
            self.fields['complex_protein'].queryset = Protein.objects.filter(pk__in=pks)
            self.fields['complex_domain'].queryset = Domain.objects.all()


ComplexCompositionFormSet = formset_factory(ComplexCompositionForm, extra=1)
formset= ComplexCompositionFormSet()
#print(formset.is_valid())

""" Step 6 : PpiForm """
class PpiForm(ModelForm):

    class Meta:
        model = Ppi
        fields = ['pdb_id','symmetry','pockets_nb']

class PpiComplexForm(ModelForm):

    class Meta:
        model = PpiComplex
        fields = ['cc_nb']

class PpiAndComplexForm(forms.Form):
    pdb_id=forms.CharField(widget=forms.TextInput(attrs={'class':'form-control'}))
    symmetry=forms.ModelChoiceField(queryset=Symmetry.objects.all(), required=True, widget=forms.Select(attrs={'class':'form-control'}), empty_label=None)
    pockets_nb=forms.IntegerField(initial=1,required=True,widget=forms.TextInput(attrs={'class':'form-control'}))
    cc_nb=forms.IntegerField(initial=1,required=True,widget=forms.TextInput(attrs={'class':'form-control'}))

""" Step 7 : CompoundForm """
class CompoundForm(ModelForm):

    class Meta:
        model = Compound
        fields = ['common_name','is_macrocycle']
        widgets = {
        'common_name': forms.TextInput(attrs={'class':'form-control', 'required': 'required'}),
        }

class RefCompoundBiblioForm(ModelForm):
    model=RefCompoundBiblio
    exclude = ['compound', 'bibliography']


TYPE_MOLECULE = (
    ('smiles', 'smiles'),
    ('iupac', 'iupac'),
    ('sketch','sketch'),
)

class BaseCompoundFormSet(BaseFormSet):
    def add_fields(self, form, index):
        super(BaseCompoundFormSet, self).add_fields(form, index)
        form.fields["compound_name"] = forms.CharField(required=True, widget=forms.TextInput(attrs={'class':'form-control','required':'required'}))
        form.fields["molecule"] = forms.CharField(required=True, widget=forms.RadioSelect(choices=TYPE_MOLECULE, attrs={'class':'form-control'}))
        form.fields["molecule_comp"] = forms.CharField(required=True, widget=forms.TextInput(attrs={'required':'required', 'class':'form-control'}))

CompoundFormSet = formset_factory(CompoundForm, formset=BaseCompoundFormSet, can_delete=True)
formset = CompoundFormSet()

""" Step 8 : TestsForm """
TEST_TYPE = (
    ('activity', 'Activity'),
    ('cytotoxicity', 'Cytotoxicity'),
    ('pk','PK'),
)

class TestsForm(forms.Form):
    test_type= forms.CharField(required=True, widget=forms.Select(choices=TEST_TYPE, attrs={'class': 'form-control'}))
    activityDesc_name=forms.ModelChoiceField(queryset=TestActivityDescription.objects.values_list('test_name', flat=True).distinct(), empty_label=None, widget=forms.Select(attrs={'class':'form-control'}))
    activityDesc_cell_line=forms.ModelChoiceField(queryset=CellLine.objects.all(), empty_label=None, widget=forms.Select(attrs={'class':'form-control'}))
    activityDesc_nb_active_compound=forms.IntegerField()
    activityDesc_type=forms.ModelChoiceField(required=False, widget=forms.RadioSelect(attrs={'class':'form-control'}),queryset=TestActivityDescription.objects.values_list('test_type', flat=True).distinct(), empty_label=None)
    activityDesc_test_modulation_type=forms.ModelChoiceField(queryset=TestActivityDescription.objects.values_list('test_modulation_type', flat=True).distinct(), empty_label=None, widget=forms.Select(attrs={'class':'form-control'}))
    activityDesc_is_primary = forms.ModelChoiceField(queryset=TestActivityDescription.objects.values_list('is_primary', flat=True).distinct(), empty_label=None, widget=forms.Select(attrs={'class':'form-control'}))
    activityDesc_protein_bound_construct = forms.ModelChoiceField(queryset=TestActivityDescription.objects.values_list('protein_bound_construct', flat=True).distinct(),  empty_label=None, widget=forms.Select(attrs={'class':'form-control'}))
    activityRes_compound = forms.ChoiceField(widget=forms.Select(attrs={'class': 'form-control'}))
    activityRes_test_modulation_type = forms.ModelChoiceField(queryset=CompoundActivityResult.objects.values_list('modulation_type', flat=True).distinct(), empty_label=None,widget=forms.Select(attrs={'class': 'form-control'}))
    activityRes_activity_type = forms.CharField(widget=forms.TextInput(attrs={'class': 'form-control'}))
    activityRes_activity = forms.IntegerField(widget=forms.NumberInput(attrs={'class': 'form-control'}))
    activityRes_inhibition_percentage = forms.IntegerField(required=False)
    cytotoxDesc_name=forms.ModelChoiceField(queryset=TestCytotoxDescription.objects.values_list('test_name', flat=True).distinct(), empty_label=None, widget=forms.Select(attrs={'class':'form-control'}))
    cytotoxDesc_cell_line=forms.ModelChoiceField(queryset=CellLine.objects.all(), empty_label=None, widget=forms.Select(attrs={'class':'form-control'}),required=False)
    cytotoxDesc_compound_concentration=forms.CharField(widget=forms.TextInput(attrs={'placeholder':'Compound concentration'}),required=False)
    cytotoxRes_compound = forms.ChoiceField(widget=forms.TextInput(attrs={'class': 'form-control'}), required=False)
    cytotoxRes_toxicity = forms.ModelChoiceField(queryset=CompoundCytotoxicityResult.objects.all(), required=False)
    pkDesc_name=forms.ModelChoiceField(queryset=TestPKDescription.objects.values_list('test_name', flat=True).distinct(), empty_label=None, widget=forms.Select(attrs={'class':'form-control'}))
    pkDesc_organism=forms.ModelChoiceField(queryset=Taxonomy.objects.all(), empty_label="Choose a corresponding organism",required=False)
    pkDesc_administration_mode=forms.CharField(widget=forms.TextInput(attrs={'placeholder':'Admnistration mode'}),required=False)
    pkDesc_dose=forms.IntegerField(required=False)
    pkDesc_dose_interval=forms.IntegerField(required=False)
    pkDesc_concentration=forms.IntegerField(required=False)
    pkRes_compound = forms.ChoiceField(widget=forms.TextInput(attrs={'class': 'form-control'}), required=False)
    pkRes_tolerated = forms.ChoiceField(widget=forms.TextInput(attrs={'class': 'form-control'}), required=False)
    pkRes_auc = forms.IntegerField(initial=1, required=False)
    pkRes_clearance = forms.DecimalField(required=False)
    pkRes_cmax = forms.DecimalField(required=False)
    pkRes_oral_bioavailability = forms.IntegerField(initial=1, required=False)
    pkRes_t_demi = forms.IntegerField(initial=1, required=False)
    pkRes_t_max = forms.IntegerField(initial=1, required=False)
    pkRes_voldistribution = forms.DecimalField(required=False)


TEST_TYPE = (
    ('activity', 'Activity'),
    ('cytotoxicity', 'Cytotoxicity'),
    ('pk','PK'),
)

UNIT_CONCENTRATION = (
    ('micro', 'µM'),
    ('nano', 'nM'),
    ('pico','pM'),
)


ADMINISTRATION_MODE = [
    ("Enteral",
        [('', "Oral"), ('', "Sublingual"), ('', "Rectal")]),
    ("Parenteral",
        [('', "Inhalational"), ('', "Intravenous"), ('', "Intramuscular"), ('', "Subcutaneous"), ('', "Intra-arterial"), ('', "Intra-articular"), ('', "Intrathecal"), ('', "Intradermal"), ('', "Transdermal")]),
    ("Local",
        [('', "Skin topical"), ('', "Intranasal"), ('', "Ocular drops"), ('', "Mucosal-throat"), ('', "Vagina"), ('', "Mouth"), ('', "Ear"), ('', "Transdermal")]),
]



class BaseTestsFormSet(BaseFormSet):
    def add_fields(self, form, index):
        super(BaseTestsFormSet, self).add_fields(form, index)
        form.fields["test_type"] = forms.CharField(required=True, widget=forms.Select(choices=TEST_TYPE, attrs={'class':'form-control'}))
        form.fields["activityDesc_name"] = forms.ModelChoiceField(queryset=TestActivityDescription.objects.values_list('test_name', flat=True).distinct(), empty_label=None, widget=forms.Select(attrs={'required':'required', 'class':'form-control'}))
        form.fields["activityDesc_cell_line"] = forms.ModelChoiceField(queryset=CellLine.objects.all(), empty_label=None,widget=forms.Select(attrs={'class': 'form-control'}))
        form.fields["activityDesc_type"] = forms.ModelChoiceField(required=False,widget=forms.Select(attrs={'class': 'form-control'}),queryset=TestActivityDescription.objects.values_list('test_type',flat=True).distinct(), empty_label=None)
        form.fields["activityDesc_test_modulation_type"] = forms.ModelChoiceField(queryset=TestActivityDescription.objects.values_list('test_modulation_type', flat=True).distinct(),empty_label=None, widget=forms.Select(attrs={'class': 'form-control'}))
        form.fields["activityDesc_protein_bound_construct"] = forms.ModelChoiceField(queryset=TestActivityDescription.objects.values_list('protein_bound_construct', flat=True).distinct(),empty_label=None, widget=forms.Select(attrs={'class': 'form-control'}))
        form.fields["activityRes_compound"] = forms.ChoiceField(widget=forms.Select(attrs={'class': 'form-control'}))
        form.fields["activityRes_activity_type"] = forms.ModelChoiceField(required=False,widget=forms.Select(attrs={'class': 'form-control'}),queryset=CompoundActivityResult.objects.values_list('activity_type',flat=True).distinct(),empty_label=None)
        form.fields["activityRes_unit_concentration"] = forms.CharField(required=True, widget=forms.Select(choices=UNIT_CONCENTRATION, attrs={'class':'form-control'}))
        form.fields["activityRes_activity"] = forms.IntegerField(forms.NumberInput(attrs={'class': 'form-control'}))
        form.fields["cytotoxDesc_name"] = forms.ModelChoiceField(queryset=TestCytotoxDescription.objects.values_list('test_name', flat=True).distinct(), empty_label=None, required=False, widget=forms.Select(attrs={'required':'required', 'class':'form-control'}))
        form.fields["cytotoxDesc_cell_line"] = forms.ModelChoiceField(queryset=CellLine.objects.all(), empty_label=None, widget=forms.Select(attrs={'class': 'form-control'}),required=False)
        form.fields["cytotoxDesc_compound_concentration"] = forms.DecimalField(required=False)
        form.fields["cytotoxRes_unit_concentration"] = forms.CharField(required=True, widget=forms.Select(choices=UNIT_CONCENTRATION, attrs={'class':'form-control'}))
        form.fields["cytotoxRes_compound"] = forms.ChoiceField(widget=forms.Select(attrs={'class': 'form-control'}),required=False)
        form.fields["cytotoxRes_toxicity"] = forms.ModelChoiceField(queryset=CompoundCytotoxicityResult.objects.values_list('toxicity', flat=True).distinct(), empty_label=None,required=False,widget=forms.Select(attrs={'class': 'form-control'}))
        form.fields["pkDesc_name"] = forms.ModelChoiceField(queryset=TestPKDescription.objects.values_list('test_name', flat=True).distinct(), empty_label=None,required=False, widget=forms.Select(attrs={'required':'required', 'class':'form-control'}))
        form.fields["pkDesc_organism"] = forms.ModelChoiceField(queryset=Taxonomy.objects.all(),empty_label=None, widget=forms.Select(attrs={'class': 'form-control'}),required=False)
        form.fields["pkDesc_administration_mode"] = forms.CharField(required=True, widget=forms.Select(choices=ADMINISTRATION_MODE, attrs={'class':'form-control'}))
        form.fields["pkDesc_dose"] = forms.IntegerField(required=False)
        form.fields["pkDesc_dose_interval"] = forms.IntegerField(required=False)
        form.fields["pkDesc_concentration"] = forms.DecimalField(required=False)
        form.fields["pkRes_compound"] = forms.ChoiceField(widget=forms.TextInput(attrs={'class': 'form-control'}), required=False)
        form.fields["pkRes_tolerated"] = forms.ChoiceField(widget=forms.TextInput(attrs={'class': 'form-control'}), required=False)
        form.fields["pkRes_auc"] = forms.IntegerField(initial=1, required=False)
        form.fields["pkRes_clearance"] = forms.DecimalField(required=False)
        form.fields["pkRes_cmax"] = forms.DecimalField(required=False)
        form.fields["pkRes_oral_bioavailability"] = forms.IntegerField(initial=1, required=False)
        form.fields["pkRes_t_demi"] = forms.IntegerField(initial=1, required=False)
        form.fields["pkRes_t_max"] = forms.IntegerField(initial=1, required=False)
        form.fields["pkRes_voldistribution"] = forms.DecimalField(required=False)

TestsFormSet = formset_factory(TestsForm, formset=BaseTestsFormSet, can_delete=True, can_order=True)
formset = TestsFormSet()