Source code for upload_step5_form

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

from app.view.forms.base_form import BaseForm



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class UploadStep5Form(BaseForm):


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    class ExperimentForm(BaseForm):

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        class Meta:

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            csrf = False




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        class BioreplicateForm(BaseForm):

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            class Meta:

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                csrf = False




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            name         = StringField('name', validators=[DataRequired()])


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            position     = StringField('position')


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            biosampleUrl = URLField('biosampleUrl')



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            isControl = BooleanField('isControl')


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            isBlank   = BooleanField('isBlank')




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        class PerturbationForm(BaseForm):

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            class Meta:

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                csrf = False




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            startTimepoint = IntegerField('startTimepoint', validators=[DataRequired()])


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



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


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


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


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




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        name           = StringField('name', validators=[DataRequired()])


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


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



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



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


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



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        bioreplicates = FieldList(FormField(BioreplicateForm))


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        perturbations = FieldList(FormField(PerturbationForm))



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

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




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


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    experiments = FieldList(FormField(ExperimentForm))



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    def validate_experiments(self, field):
        # Local validation:
        names = [e['name'] for e in field.data]
        self._validate_uniqueness("names are not unique", names)

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