How to use the jsonmodels.fields.ListField function in jsonmodels

# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from jsonmodels import models, fields

__author__ = "ckopanos"


class GnomADCoverage(models.Base):
    version = fields.StringField(help_text="Version")
    coverage_mean = fields.ListField(help_text="Mean coverage",
                                     items_types=(float, type(None)), required=False, nullable=True)
    coverage_median = fields.ListField(help_text="Median coverage",
                                       items_types=(float, type(None)), required=False, nullable=True)
    coverage_20_frequency = fields.ListField(help_text="Proportion of samples with over 20x",
                                             items_types=(float, type(None)),
                                             required=False, nullable=True)


class GnomAD(models.Base):
    version = fields.StringField(help_text="Version")
    ac = fields.IntField(help_text="Allele Count", required=False, nullable=True)
    an = fields.IntField(help_text="Allele Number", required=False, nullable=True)
    ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True)
    an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True)
    af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True)
    ac_afr = fields.IntField(help_text="Allele Count African", required=False, nullable=True)
    ac_amr = fields.IntField(help_text="Allele Count American", required=False, nullable=True)
    ac_asj = fields.IntField(help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True)
    ac_eas = fields.IntField(help_text="Allele Count East Asian", required=False, nullable=True)
    ac_fin = fields.IntField(help_text="Allele Count European (Finnish)", required=False, nullable=True)

primary_site_freq = fields.ListField(items_types=(int, str, float), help_text="Primary site frequency", required=False, nullable=True)
    description = fields.ListField(items_types=(str,), help_text="Description", required=False, nullable=True)
    accession_number = fields.ListField(items_types=(str,), help_text="Accession number", required=False, nullable=True)
    fathmm_prediction = fields.StringField(help_text="FATHMM prediction", required=False, nullable=True)
    fathmm_score = fields.FloatField(help_text="FATHMM score", required=False, nullable=True)
    num_entries = fields.IntField(help_text="Number of entries", required=False, nullable=True)
    num_samples = fields.IntField(help_text="Number of samples", required=False, nullable=True)
    gene = fields.ListField(items_types=(str,), help_text="Gene", required=False, nullable=True)

    fathmm_mkl_coding_score = fields.FloatField(help_text="FATHMM_MKL coding score", required=False, nullable=True)
    fathmm_mkl_coding_groups = fields.StringField(help_text="FATHMM_MKL coding groups", required=False, nullable=True)
    fathmm_mkl_non_coding_score = fields.FloatField(help_text="FATHMM_MKL non coding score", required=False,
                                                    nullable=True)
    fathmm_mkl_non_coding_groups = fields.StringField(help_text="FATHMM_MKL non coding groups", required=False,
                                                      nullable=True)
    whole_exome_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole exome frequency", required=False,
                                        nullable=True)
    whole_genome_reseq_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole genome reseq frequency",
                                               required=False, nullable=True)

    resistance_mutation = fields.ListField(items_types=(str,), help_text="Resistance mutation", required=False,
                                           nullable=True)
    drug_entries = fields.ListField(items_types=(CosmicLicensedDrugEntry,), help_text="Drug entries", required=False,
                                    nullable=True)


class ComsicPublicDetails(models.Base):
    num_samples = fields.IntField(help_text='Number of samples')
    id = fields.StringField(help_text='Cosmic ID')
    is_consistent = fields.BoolField(help_text='Cosmic ID is consistent across databases')

mutationassessor_score = fields.ListField(items_types=(float,), help_text="MutationAssessor score",
                                              required=False)
    mutationassessor_score_rankscore = fields.ListField(items_types=(float,),
                                                        help_text="MutationAssessor rankscore", required=False,
                                                        nullable=True)
    fathmm_mkl_coding_pred = fields.ListField(items_types=(str,),
                                              help_text="FATHMM-MKL coding prediction", required=False, nullable=True)
    fathmm_mkl_coding_score = fields.ListField(items_types=(float,), help_text="FATHMM-MKL coding score",
                                               required=False)
    fathmm_mkl_coding_rankscore = fields.ListField(items_types=(float,),
                                                   help_text="FATHMM-MKL coding rankscore", required=False,
                                                   nullable=True)
    fathmm_pred = fields.ListField(items_types=(str,), help_text="FATHMM prediction", required=False, nullable=True)
    fathmm_score = fields.ListField(items_types=(float,), help_text="FATHMM score",
                                    required=False)
    fathmm_converted_rankscore = fields.ListField(items_types=(float,), help_text="FATHMM converted rankscore",
                                                  required=False, nullable=True)
    sift_converted_rankscore = fields.ListField(items_types=(float,), help_text="SIFT converted rankscore",
                                                required=False)
    metasvm_pred = fields.ListField(items_types=(str,), help_text="MetaSVM prediction",
                                    required=False)
    metasvm_score = fields.ListField(items_types=(float,), help_text="MetaSVM score", required=False, nullable=True)
    metasvm_rankscore = fields.ListField(items_types=(float,), help_text="MetaSVM rankscore",
                                         required=False)
    metalr_pred = fields.ListField(items_types=(str,), help_text="MetalR prediction", required=False, nullable=True)
    metalr_score = fields.ListField(items_types=(float,), help_text="MetalR score", required=False, nullable=True)
    metalr_rankscore = fields.ListField(items_types=(float,), help_text="MetalR rankscore", required=False,
                                        nullable=True)
    provean_pred = fields.ListField(items_types=(str,), help_text="Provean prediction",
                                    required=False)
    provean_score = fields.ListField(items_types=(float,), help_text="Provean score",
                                     required=False)

class TranscriptItem(models.Base):
    name = fields.StringField(help_text="Transcript")
    coding_impact = fields.StringField(help_text="Coding impact", required=False, nullable=True)
    function = fields.ListField(help_text="Function", items_types=(str,), required=False, nullable=True)
    hgvs = fields.StringField(required=False, help_text="HGVS cDNA level", nullable=True)
    hgvs_p1 = fields.StringField(required=False, nullable=True)
    hgvs_p3 = fields.StringField(required=False, nullable=True)
    hgvs_notation = fields.StringField(help_text="HGVS notation", required=False, nullable=True)
    location = fields.StringField(help_text="Location", required=False, nullable=True)
    coding_location = fields.StringField(help_text="Coding location", required=False, nullable=True)
    canonical = fields.BoolField(help_text="Canonical", required=False, nullable=True)
    gene_symbol = fields.StringField(help_text="Gene symbol", required=False, nullable=True)


class Transcript(models.Base):
    items = fields.ListField(help_text='Transcripts', items_types=(TranscriptItem,), required=False)
    version = fields.StringField(help_text="Version")

num_entries = fields.IntField(help_text="Number of entries", required=False, nullable=True)
    num_samples = fields.IntField(help_text="Number of samples", required=False, nullable=True)
    gene = fields.ListField(items_types=(str,), help_text="Gene", required=False, nullable=True)

    fathmm_mkl_coding_score = fields.FloatField(help_text="FATHMM_MKL coding score", required=False, nullable=True)
    fathmm_mkl_coding_groups = fields.StringField(help_text="FATHMM_MKL coding groups", required=False, nullable=True)
    fathmm_mkl_non_coding_score = fields.FloatField(help_text="FATHMM_MKL non coding score", required=False,
                                                    nullable=True)
    fathmm_mkl_non_coding_groups = fields.StringField(help_text="FATHMM_MKL non coding groups", required=False,
                                                      nullable=True)
    whole_exome_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole exome frequency", required=False,
                                        nullable=True)
    whole_genome_reseq_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole genome reseq frequency",
                                               required=False, nullable=True)

    resistance_mutation = fields.ListField(items_types=(str,), help_text="Resistance mutation", required=False,
                                           nullable=True)
    drug_entries = fields.ListField(items_types=(CosmicLicensedDrugEntry,), help_text="Drug entries", required=False,
                                    nullable=True)


class ComsicPublicDetails(models.Base):
    num_samples = fields.IntField(help_text='Number of samples')
    id = fields.StringField(help_text='Cosmic ID')
    is_consistent = fields.BoolField(help_text='Cosmic ID is consistent across databases')




class CosmicPublic(models.Base):
    version = fields.StringField(help_text="Version")
    items = fields.ListField(items_types=(ComsicPublicDetails, ), help_text="Details", required=False, nullable=True)

def iterate_embedded_model_instances(self):
        for name, field in self.iterate_over_set_fields():
            if isinstance(field, fields.EmbeddedField):
                subobjs = (getattr(self, name),)
            elif isinstance(field, fields.ListField):
                subobjs = getattr(self, name)
            else:
                continue

            for subobj in subobjs:
                if isinstance(subobj, ModelBase):
                    yield subobj

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from jsonmodels import models, fields

__author__ = "ckopanos"


class ThousandGenomes(models.Base):
    version = fields.StringField(help_text="Version")
    ac = fields.ListField(items_types=(int,), help_text="Allele Count", required=False, nullable=True)
    af = fields.ListField(items_types=(float,), help_text="Allele Frequency", required=False, nullable=True)
    an = fields.ListField(items_types=(int,), help_text="Allele Number", required=False, nullable=True)
    ns = fields.ListField(items_types=(int,), help_text="Number of Samples", required=False, nullable=True)
    afr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency African", required=False, nullable=True)
    amr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency American", required=False,
                              nullable=True)
    eas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency East Asian", required=False,
                              nullable=True)
    eur_af = fields.ListField(items_types=(float,), help_text="Allele Frequency European", required=False,
                              nullable=True)
    sas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency South Asian", required=False,
                              nullable=True)
    main_data = fields.StringField(help_text="Main data point", required=False, nullable=True)

sift_prediction = fields.StringField(help_text="SIFT prediction", required=False, nullable=True)
    phylop100way_vertebrate = fields.ListField(items_types=(float,), help_text="phyloP100way vertebrate",
                                               required=False)
    phylop46way_placental = fields.ListField(items_types=(float,), help_text="phyloP46way placental",
                                             required=False)
    phylop46way_primate = fields.ListField(items_types=(float,), help_text="phyloP46way primate",
                                           required=False)
    mutationtaster_converted_rankscore = fields.ListField(items_types=(float,),
                                                          help_text="MutationTaster converted rankscore",
                                                          required=False, nullable=True)
    mutationassessor_pred = fields.ListField(items_types=(str,),
                                             help_text="MutationAssessor prediction",
                                             required=False)
    mutationassessor_score = fields.ListField(items_types=(float,), help_text="MutationAssessor score",
                                              required=False)
    mutationassessor_score_rankscore = fields.ListField(items_types=(float,),
                                                        help_text="MutationAssessor rankscore", required=False,
                                                        nullable=True)
    fathmm_mkl_coding_pred = fields.ListField(items_types=(str,),
                                              help_text="FATHMM-MKL coding prediction", required=False, nullable=True)
    fathmm_mkl_coding_score = fields.ListField(items_types=(float,), help_text="FATHMM-MKL coding score",
                                               required=False)
    fathmm_mkl_coding_rankscore = fields.ListField(items_types=(float,),
                                                   help_text="FATHMM-MKL coding rankscore", required=False,
                                                   nullable=True)
    fathmm_pred = fields.ListField(items_types=(str,), help_text="FATHMM prediction", required=False, nullable=True)
    fathmm_score = fields.ListField(items_types=(float,), help_text="FATHMM score",
                                    required=False)
    fathmm_converted_rankscore = fields.ListField(items_types=(float,), help_text="FATHMM converted rankscore",
                                                  required=False, nullable=True)
    sift_converted_rankscore = fields.ListField(items_types=(float,), help_text="SIFT converted rankscore",
                                                required=False)

mutationassessor_pred = fields.ListField(items_types=(str,),
                                             help_text="MutationAssessor prediction",
                                             required=False)
    mutationassessor_score = fields.ListField(items_types=(float,), help_text="MutationAssessor score",
                                              required=False)
    mutationassessor_score_rankscore = fields.ListField(items_types=(float,),
                                                        help_text="MutationAssessor rankscore", required=False,
                                                        nullable=True)
    fathmm_mkl_coding_pred = fields.ListField(items_types=(str,),
                                              help_text="FATHMM-MKL coding prediction", required=False, nullable=True)
    fathmm_mkl_coding_score = fields.ListField(items_types=(float,), help_text="FATHMM-MKL coding score",
                                               required=False)
    fathmm_mkl_coding_rankscore = fields.ListField(items_types=(float,),
                                                   help_text="FATHMM-MKL coding rankscore", required=False,
                                                   nullable=True)
    fathmm_pred = fields.ListField(items_types=(str,), help_text="FATHMM prediction", required=False, nullable=True)
    fathmm_score = fields.ListField(items_types=(float,), help_text="FATHMM score",
                                    required=False)
    fathmm_converted_rankscore = fields.ListField(items_types=(float,), help_text="FATHMM converted rankscore",
                                                  required=False, nullable=True)
    sift_converted_rankscore = fields.ListField(items_types=(float,), help_text="SIFT converted rankscore",
                                                required=False)
    metasvm_pred = fields.ListField(items_types=(str,), help_text="MetaSVM prediction",
                                    required=False)
    metasvm_score = fields.ListField(items_types=(float,), help_text="MetaSVM score", required=False, nullable=True)
    metasvm_rankscore = fields.ListField(items_types=(float,), help_text="MetaSVM rankscore",
                                         required=False)
    metalr_pred = fields.ListField(items_types=(str,), help_text="MetalR prediction", required=False, nullable=True)
    metalr_score = fields.ListField(items_types=(float,), help_text="MetalR score", required=False, nullable=True)
    metalr_rankscore = fields.ListField(items_types=(float,), help_text="MetalR rankscore", required=False,
                                        nullable=True)
    provean_pred = fields.ListField(items_types=(str,), help_text="Provean prediction",

class CosmicLicensedDetails(models.Base):
    entry_type = fields.StringField(help_text="Entry type", required=False, nullable=True)
    cosmic_id = fields.ListField(items_types=(str, dict,), help_text="Cosmic ID", required=False, nullable=True)
    pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False,
                                          nullable=True)
    histology_freq = fields.ListField(items_types=(int, str, float), help_text="Histology frequency", required=False,
                                      nullable=True)
    genome_wide_screen_freq = fields.ListField(items_types=(int, str, float), help_text="Histology frequency", required=False,
                                               nullable=True)
    loh_freq = fields.ListField(items_types=(int, str, float), help_text="LOH frequency", required=False, nullable=True)
    age_freq = fields.ListField(items_types=(int, str, float), help_text="Age frequency", required=False, nullable=True)
    zygosity_freq = fields.ListField(items_types=(int, str, float), help_text="Zygosity frequency", required=False,
                                     nullable=True)
    tumour_origin_freq = fields.ListField(items_types=(int, str, float,), help_text="Tumour original frequency", required=False,
                                          nullable=True)
    somatic_status_freq = fields.ListField(items_types=(int, str, float), help_text="Somatic status frequency", required=False,
                                           nullable=True)
    primary_site_freq = fields.ListField(items_types=(int, str, float), help_text="Primary site frequency", required=False, nullable=True)
    description = fields.ListField(items_types=(str,), help_text="Description", required=False, nullable=True)
    accession_number = fields.ListField(items_types=(str,), help_text="Accession number", required=False, nullable=True)
    fathmm_prediction = fields.StringField(help_text="FATHMM prediction", required=False, nullable=True)
    fathmm_score = fields.FloatField(help_text="FATHMM score", required=False, nullable=True)
    num_entries = fields.IntField(help_text="Number of entries", required=False, nullable=True)
    num_samples = fields.IntField(help_text="Number of samples", required=False, nullable=True)
    gene = fields.ListField(items_types=(str,), help_text="Gene", required=False, nullable=True)

    fathmm_mkl_coding_score = fields.FloatField(help_text="FATHMM_MKL coding score", required=False, nullable=True)
    fathmm_mkl_coding_groups = fields.StringField(help_text="FATHMM_MKL coding groups", required=False, nullable=True)
    fathmm_mkl_non_coding_score = fields.FloatField(help_text="FATHMM_MKL non coding score", required=False,
                                                    nullable=True)