forms.py

import datetime
from functools import partial

from django import forms
from haystack.forms import ModelSearchForm
from haystack.query import SearchQuerySet
from Bio.Alphabet import IUPAC

from public_interface.models import Genes, Vouchers


DateInput = partial(forms.DateInput, {'class': 'datepicker form-control',
                                      'placeholder': 'Type or pick a date'})


class SequencesAdminForm(forms.ModelForm):
    def clean_sequences(self):
        valid_letters = set(IUPAC.ambiguous_dna.letters.upper() + 'N?-')
        sequence = str(self.cleaned_data['sequences'])
        for nucleotide in sequence:
            if nucleotide == ' ':
                self.add_error('sequences', "White spaces are not valid. "
                                            "Cannot save this sequence")
            elif not valid_letters.issuperset(nucleotide.upper()):
                self.add_error('sequences', "The character {} is not valid. "
                                            "Cannot save this sequence".format(nucleotide))
        return sequence


class AdvancedSearchForm(ModelSearchForm):
    NULL = 'Select'
    MALE = 'male'
    FEMALE = 'female'
    LARVA = 'larva'
    WORKER = 'worker'
    QUEEN = 'queen'
    UNKNOWN = 'unknown'
    SEX_CHOICES = (
        (NULL, 'Select'),
        (MALE, 'male'),
        (FEMALE, 'female'),
        (LARVA, 'larva'),
        (WORKER, 'worker'),
        (QUEEN, 'queen'),
        (UNKNOWN, 'unknown'),
    )

    NULL = 'Select'
    DONT_KNOW = 'unknown'
    YES = 'yes'
    NO = 'not'
    TYPE_SPECIES_CHOICES = (
        (NULL, 'Select'),
        (DONT_KNOW, 'unknown'),
        (YES, 'yes'),
        (NO, 'not'),
    )

    NULL = 'Select'
    SPREAD = 'spread'
    ENVELOPE = 'in envelope'
    PHOTO = 'only photo'
    NONE = 'no voucher'
    DESTROYED = 'destroyed'
    LOST = 'lost'
    VOUCHER_CHOICES = (
        (NULL, 'Select'),
        (SPREAD, 'spread'),
        (ENVELOPE, 'in envelope'),
        (PHOTO, 'only photo'),
        (NONE, 'no voucher'),
        (DESTROYED, 'destroyed'),
        (LOST, 'lost'),
        (UNKNOWN, 'unknown'),
    )
    code = forms.CharField(label="Code in voseq", max_length=100, required=False)
    orden = forms.CharField(label="Order", max_length=100, required=False)
    superfamily = forms.CharField(label="Superfamily", max_length=100, required=False)
    family = forms.CharField(label="Family", max_length=100, required=False)
    subfamily = forms.CharField(label="Subfamily", max_length=100, required=False)
    tribe = forms.CharField(label="Tribe", max_length=100, required=False)
    subtribe = forms.CharField(label="Subtribe", max_length=100, required=False)
    genus = forms.CharField(label="Genus", max_length=100, required=False)
    species = forms.CharField(label="Species", max_length=100, required=False)
    subspecies = forms.CharField(label="Subspecies", max_length=100, required=False)
    country = forms.CharField(label="Country", max_length=100, required=False)
    specific_locality = forms.CharField(label="Specific Locality", max_length=250, required=False)
    type_species = forms.ChoiceField(label="Type species", choices=TYPE_SPECIES_CHOICES,
                                     widget=forms.Select(attrs={'class': 'form-control'}), required=False)
    latitude = forms.FloatField(label="Latitude", required=False)
    longitude = forms.FloatField(label="Longitude", required=False)
    max_altitude = forms.IntegerField(label="Maximum altitude", required=False)
    min_altitude = forms.IntegerField(label="Minimum altitude", required=False)
    collector = forms.CharField(label="Collector", max_length=100, required=False)
    date_collection = forms.DateField(
        label="Date of collection start",
        required=False,
        widget=DateInput(),
        error_messages={'invalid': 'Enter valid date: YYYY-mm-dd'},
    )
    date_collection_end = forms.DateField(
        label="Date of collection end",
        required=False,
        widget=DateInput(),
        error_messages={'invalid': 'Enter valid date: YYYY-mm-dd'},
    )
    extraction = forms.CharField(label="Extraction", max_length=50, help_text="Number of extraction event.", required=False)
    extraction_tube = forms.CharField(label="Extraction tube", max_length=50, help_text="Tube containing DNA extract.", required=False)
    date_extraction = forms.DateField(label="Date of extraction", required=False, widget=DateInput(),
                                      error_messages={'invalid': 'Enter valid date: YYYY-mm-dd'})
    extractor = forms.CharField(label="Extractor", max_length=100, required=False)
    voucher_locality = forms.CharField(label="Voucher locality", max_length=200, required=False)
    published_in = forms.CharField(label="Published in", required=False)
    notes = forms.CharField(label="Notes", required=False)
    latest_editor = forms.CharField(label="Latest editor", required=False)
    hostorg = forms.CharField(label="Host organism", max_length=200, help_text="Hostplant or other host.", required=False)
    sex = forms.ChoiceField(label="Sex", choices=SEX_CHOICES, required=False,
                            widget=forms.Select(attrs={'class': 'form-control'}))
    voucher = forms.ChoiceField(label="Voucher", choices=VOUCHER_CHOICES, required=False,
                                widget=forms.Select(attrs={'class': 'form-control'}))
    voucher_code = forms.CharField(label="Alternative voucher code", max_length=100, help_text="Original code of voucher specimen.", required=False)
    code_bold = forms.CharField(label="Code in BOLD database", max_length=100, help_text="Optional code for specimens kept in the BOLD database.",
                                required=False)
    determined_by = forms.CharField(label="Determined by", max_length=100, help_text="Person that identified the taxon for this specimen.",
                                    required=False)
    author = forms.CharField(label="Author", max_length=100,
                             help_text="Person that described this taxon.", required=False)

    # Sequences model
    YES = 'y'
    NO = 'n'
    GENBANK_CHOICES = (
        (YES, 'Yes'),
        (NO, 'No'),
    )
    gene_code = forms.ModelChoiceField(
        Genes.objects.all().order_by('gene_code'),
        required=False,
        widget=forms.Select(attrs={'class': 'form-control'}),
        empty_label='Select',
    )
    genbank = forms.ChoiceField(widget=forms.RadioSelect, choices=GENBANK_CHOICES, required=False)
    accession = forms.CharField(max_length=100, required=False)
    lab_person = forms.CharField(max_length=100, required=False)

    def no_query_found(self):
        sqs = SearchQuerySet.none
        return sqs

    def search(self):
        keywords, sequence_keywords = self.clean_search_keywords()
        sqs = ''
        if keywords and not sequence_keywords:
            sqs = Vouchers.objects.filter(**keywords)
            # print(results)
            # sqs = SearchQuerySet().using('vouchers').filter(**keywords)
        elif sequence_keywords and not keywords:
            sqs = SearchQuerySet().using('advanced_search').filter(
                **sequence_keywords)
            sqs = filter_results_from_sequence_table(sqs)
        elif sequence_keywords and keywords:
            sqs = SearchQuerySet().using('vouchers').filter(**keywords)
            if sqs:
                voucher_code_list = get_list_of_codes(sqs)
                sqs = SearchQuerySet().using("advanced_search").filter(
                    **sequence_keywords).filter(code__in=voucher_code_list)
            else:
                self.no_query_found()
            sqs = filter_results_from_sequence_table(sqs)

        if sqs:
            return sqs
        else:
            self.no_query_found()

    def clean_search_keywords(self):
        keywords = {}
        sequence_keywords = {}
        for k, v in self.cleaned_data.items():
            if v != '' and v is not None:
                # remove after adding this to index
                if v == 'Select':
                    continue
                if k in ['date_collection', 'date_collection_end', 'date_extraction']:
                    v = datetime.date.strftime(v, "%Y-%m-%d")
                if k == 'models':
                    continue
                if k in ['lab_person', 'accession']:
                    sequence_keywords[k] = v
                if k == 'gene_code':
                    sequence_keywords[k] = v.gene_code
                if k == 'genbank' and v == 'y':
                    sequence_keywords[k] = 'true'
                elif k == 'genbank':
                    sequence_keywords[k] = 'false'
                if k not in ['lab_person', 'accession', 'genbank', 'gene_code']:
                    keywords[k] = v

        return keywords, sequence_keywords


def get_list_of_codes(sqs):
    voucher_codes = []
    for item in sqs:
        if item not in voucher_codes:
            voucher_codes.append(item.code)
    return voucher_codes


def filter_results_from_sequence_table(sqs):
    """Need to avoid returning duplicated voucher results"""
    facet_counts = sqs.facet('code', size=90000).facet_counts()
    voucher_codes_count = facet_counts['fields']['code']
    if voucher_codes_count:
        voucher_codes = [item[0] for item in voucher_codes_count]
        filtered_sqs = SearchQuerySet().using("vouchers").filter(code__in=voucher_codes)
        return filtered_sqs
    else:
        return sqs


# The following form is for the admin site bacth_changes action
# It would be nice not to repeat the lines from the previous
# model, but...
class BatchChangesForm(forms.Form):
    '''
    class Meta:
        model = Vouchers
        fields = ['orden', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe',
                  'genus', 'species', 'subspecies', 'type_species', 'sex', 'author',
                  'determined_by', 'published_in', 'country', 'specific_locality', 'latitude',
                  'longitude', 'max_altitude', 'min_altitude', 'date_collection',
                  'date_collection_end', 'collector',
                  'hostorg', 'date_extraction', 'extractor', 'extraction', 'extraction_tube',
                  'voucher', 'voucher_locality', 'latest_editor', 'edits', 'notes']
    '''

    NULL = None
    MALE = 'male'
    FEMALE = 'female'
    LARVA = 'larva'
    WORKER = 'worker'
    QUEEN = 'queen'
    SEX_CHOICES = (
        (NULL, 'Select'),
        (MALE, 'male'),
        (FEMALE, 'female'),
        (LARVA, 'larva'),
        (WORKER, 'worker'),
        (QUEEN, 'queen'),
    )

    NULL = None
    DONT_KNOW = 'unknown'
    YES = 'yes'
    NO = 'not'
    TYPE_SPECIES_CHOICES = (
        (NULL, 'Select'),
        (DONT_KNOW, 'unknown'),
        (YES, 'yes'),
        (NO, 'not'),
    )
    NULL = None
    SPREAD = 'spread'
    ENVELOPE = 'in envelope'
    PHOTO = 'only photo'
    NONE = 'no voucher'
    DESTROYED = 'destroyed'
    LOST = 'lost'
    VOUCHER_CHOICES = (
        (NULL, 'Select'),
        (SPREAD, 'spread'),
        (ENVELOPE, 'in envelope'),
        (PHOTO, 'only photo'),
        (NONE, 'no voucher'),
        (DESTROYED, 'destroyed'),
        (LOST, 'lost'),
    )
    code = forms.CharField(label="Code in voseq", max_length=100, required=False)
    orden = forms.CharField(label="Order", max_length=100, required=False)
    superfamily = forms.CharField(label="Superfamily", max_length=100, required=False)
    family = forms.CharField(label="Family", max_length=100, required=False)
    subfamily = forms.CharField(label="Subfamily", max_length=100, required=False)
    tribe = forms.CharField(label="Tribe", max_length=100, required=False)
    subtribe = forms.CharField(label="Subtribe", max_length=100, required=False)
    genus = forms.CharField(label="Genus", max_length=100, required=False)
    species = forms.CharField(label="Species", max_length=100, required=False)
    subspecies = forms.CharField(label="Subspecies", max_length=100, required=False)
    country = forms.CharField(label="Country", max_length=100, required=False)
    specific_locality = forms.CharField(label="Specific Locality", max_length=250, required=False)
    type_species = forms.ChoiceField(label="Type species", choices=TYPE_SPECIES_CHOICES, widget=forms.Select, required=False)
    latitude = forms.FloatField(label="Latitude", required=False)
    longitude = forms.FloatField(label="Longitude", required=False)
    max_altitude = forms.IntegerField(label="Maximum altitude", required=False)
    min_altitude = forms.IntegerField(label="Minimum altitude", required=False)
    collector = forms.CharField(label="Collector", max_length=100, required=False)
    date_collection = forms.DateField(label="Date of collection start", required=False)
    date_collection_end = forms.DateField(label="Date of collection end", required=False)
    extraction = forms.CharField(label="Extraction", max_length=50, help_text="Number of extraction event.", required=False)
    extraction_tube = forms.CharField(label="Extraction tube", max_length=50, help_text="Tube containing DNA extract.", required=False)
    date_extraction = forms.DateField(label="Date extraction", required=False)
    extractor = forms.CharField(label="Extractor", max_length=100, required=False)
    voucher_locality = forms.CharField(label="Voucher locality", max_length=200, required=False)
    published_in = forms.CharField(label="Published in", required=False)
    notes = forms.CharField(label="Notes", required=False)
    latest_editor = forms.CharField(label="Latest editor", required=False)
    hostorg = forms.CharField(label="Host organism", max_length=200, help_text="Hostplant or other host.", required=False)
    sex = forms.ChoiceField(label="Sex", choices=SEX_CHOICES, required=False)
    voucher = forms.ChoiceField(label="Voucher", choices=VOUCHER_CHOICES, required=False)
    voucher_code = forms.CharField(label="Alternative voucher code", max_length=100, help_text="Original code of voucher specimen.", required=False)
    code_bold = forms.CharField(label="Code in BOLD database", max_length=100, help_text="Optional code for specimens kept in the BOLD database.",
                                required=False)
    determined_by = forms.CharField(label="Determined by", max_length=100, help_text="Person that identified the taxon for this specimen.",
                                    required=False)
    author = forms.CharField(label="Author", max_length=100, help_text="Person that described this taxon.", required=False)