Source code for app.view.forms.upload_step5_form

from wtforms import (
    BooleanField,
    FieldList,
    FormField,
    HiddenField,
    IntegerField,
    SelectField,
    SelectMultipleField,
    StringField,
    TextAreaField,
    URLField,
)
from wtforms.validators import DataRequired, ValidationError, Length

from app.view.forms.base_form import BaseForm



[docs]
class UploadStep5Form(BaseForm):

[docs]
    class Meta:

[docs]
        csrf_time_limit = None




[docs]
    class ExperimentForm(BaseForm):

[docs]
        class Meta:

[docs]
            csrf = False




[docs]
        class BioreplicateForm(BaseForm):

[docs]
            class Meta:

[docs]
                csrf = False




[docs]
            name         = StringField('name', validators=[DataRequired(), Length(max=100)])


[docs]
            position     = StringField('position', validators=[Length(max=100)])


[docs]
            biosampleUrl = URLField('biosampleUrl')




[docs]
        class PerturbationForm(BaseForm):

[docs]
            class Meta:

[docs]
                csrf = False



            # Note: converted to seconds when creating perturbation

[docs]
            startTime = IntegerField('startTime', validators=[DataRequired()])


[docs]
            endTime   = IntegerField('endTime',   validators=[DataRequired()])



[docs]
            description = TextAreaField('description', validators=[DataRequired()])



[docs]
            removedCompartmentName = SelectField('removedCompartmentName', choices=[], validate_choice=False)


[docs]
            addedCompartmentName   = SelectField('addedCompartmentName',   choices=[], validate_choice=False)


[docs]
            oldCommunityName       = SelectField('oldCommunityName',       choices=[], validate_choice=False)


[docs]
            newCommunityName       = SelectField('newCommunityName',       choices=[], validate_choice=False)




[docs]
        publicId       = HiddenField('publicId')


[docs]
        name           = StringField('name', validators=[DataRequired(), Length(max=100)])


[docs]
        description    = TextAreaField('description', validators=[DataRequired()])


[docs]
        timepointCount = IntegerField('timepointCount', validators=[DataRequired()])



[docs]
        cultivationMode = SelectField('cultivationMode', choices=[
            ('batch',     "Batch"),
            ('fed-batch', "Fed-batch"),
            ('chemostat', "Chemostat"),
            ('other',     "Other"),
        ])



[docs]
        communityName = SelectField(
            'communityName',
            validators=[DataRequired()],
            choices=[],
            validate_choice=False,
        )


[docs]
        compartmentNames = SelectMultipleField(
            'compartmentNames',
            validators=[DataRequired()],
            choices=[],
            validate_choice=False,
        )



[docs]
        bioreplicates = FieldList(FormField(BioreplicateForm))


[docs]
        perturbations = FieldList(FormField(PerturbationForm))



[docs]
        def validate_bioreplicates(self, field):
            names = [b['name'] for b in field.data]
            self._validate_uniqueness("name", "names are not unique", names)

            if len(names) == 0:
                raise ValidationError("at least one is required")




[docs]
    timeUnits = SelectField('timeUnits', choices=[
        ('d', 'Days (d)'),
        ('h', 'Hours (h)'),
        ('m', 'Minutes (m)'),
        ('s', 'Seconds (s)'),
    ])


[docs]
    experiments = FieldList(FormField(ExperimentForm))



[docs]
    def validate_experiments(self, field):
        # Local validation:
        names = [e['name'] for e in field.data]

        try:
            self._validate_uniqueness("experiment_names", "names are not unique", names)
        except ValidationError as e:
            for field in self.experiments:
                if field.data['name'] in self._duplicated_attributes['experiment_names']:
                    field.form_errors.append('name: not unique')
            raise e

        # Global bioreplicate validation:
        names = [
            bioreplicate['name']
            for experiment in field.data
            for bioreplicate in experiment['bioreplicates']
        ]
        self._validate_uniqueness("bioreplicate_names", "bioreplicate names are not globally unique", names)