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SP-1985 Accepting None as a possible list item on DBNSFP #13

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Merged
kchatzikok merged 1 commit into from
Dec 15, 2020
Merged

SP-1985 Accepting None as a possible list item on DBNSFP #13

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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -105,3 +105,4 @@ ENV/
#jetbrains ide

.idea
.envrc
101 changes: 51 additions & 50 deletions varsome_api/models/elements/dbnsfp.py
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Expand Up @@ -13,112 +13,113 @@
# limitations under the License.

from jsonmodels import models, fields

from varsome_api.models.fields import NullableItemListField
__author__ = "ckopanos"



class DbNSFP(models.Base):
version = fields.StringField(help_text="Version")
mutationtaster_pred = fields.ListField(items_types=(str,), help_text="MutationTaster Prediction",
mutationtaster_pred = NullableItemListField(items_types=(str,), help_text="MutationTaster Prediction",
required=False)
mutationtaster_score = fields.ListField(items_types=(float,),
mutationtaster_score = NullableItemListField(items_types=(float,),
help_text="MutationTaster Accuracy", required=False, nullable=True)
sift_score = fields.ListField(items_types=(float,), help_text="SIFT score", required=False, nullable=True)
sift_score = NullableItemListField(items_types=(float,), help_text="SIFT score", 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",
phylop100way_vertebrate = NullableItemListField(items_types=(float,), help_text="phyloP100way vertebrate",
required=False)
phylop46way_placental = fields.ListField(items_types=(float,), help_text="phyloP46way placental",
phylop46way_placental = NullableItemListField(items_types=(float,), help_text="phyloP46way placental",
required=False)
phylop46way_primate = fields.ListField(items_types=(float,), help_text="phyloP46way primate",
phylop46way_primate = NullableItemListField(items_types=(float,), help_text="phyloP46way primate",
required=False)
mutationtaster_converted_rankscore = fields.ListField(items_types=(float,),
mutationtaster_converted_rankscore = NullableItemListField(items_types=(float,),
help_text="MutationTaster converted rankscore",
required=False, nullable=True)
mutationassessor_pred = fields.ListField(items_types=(str,),
mutationassessor_pred = NullableItemListField(items_types=(str,),
help_text="MutationAssessor prediction",
required=False)
mutationassessor_score = fields.ListField(items_types=(float,), help_text="MutationAssessor score",
mutationassessor_score = NullableItemListField(items_types=(float,), help_text="MutationAssessor score",
required=False)
mutationassessor_score_rankscore = fields.ListField(items_types=(float,),
mutationassessor_score_rankscore = NullableItemListField(items_types=(float,),
help_text="MutationAssessor rankscore", required=False,
nullable=True)
fathmm_mkl_coding_pred = fields.ListField(items_types=(str,),
fathmm_mkl_coding_pred = NullableItemListField(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",
fathmm_mkl_coding_score = NullableItemListField(items_types=(float,), help_text="FATHMM-MKL coding score",
required=False)
fathmm_mkl_coding_rankscore = fields.ListField(items_types=(float,),
fathmm_mkl_coding_rankscore = NullableItemListField(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",
fathmm_pred = NullableItemListField(items_types=(str,), help_text="FATHMM prediction", required=False, nullable=True)
fathmm_score = NullableItemListField(items_types=(float,), help_text="FATHMM score",
required=False)
fathmm_converted_rankscore = fields.ListField(items_types=(float,), help_text="FATHMM converted rankscore",
fathmm_converted_rankscore = NullableItemListField(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",
sift_converted_rankscore = NullableItemListField(items_types=(float,), help_text="SIFT converted rankscore",
required=False)
metasvm_pred = fields.ListField(items_types=(str,), help_text="MetaSVM prediction",
metasvm_pred = NullableItemListField(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",
metasvm_score = NullableItemListField(items_types=(float,), help_text="MetaSVM score", required=False, nullable=True)
metasvm_rankscore = NullableItemListField(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,
metalr_pred = NullableItemListField(items_types=(str,), help_text="MetalR prediction", required=False, nullable=True)
metalr_score = NullableItemListField(items_types=(float,), help_text="MetalR score", required=False, nullable=True)
metalr_rankscore = NullableItemListField(items_types=(float,), help_text="MetalR rankscore", required=False,
nullable=True)
provean_pred = fields.ListField(items_types=(str,), help_text="Provean prediction",
provean_pred = NullableItemListField(items_types=(str,), help_text="Provean prediction",
required=False)
provean_score = fields.ListField(items_types=(float,), help_text="Provean score",
provean_score = NullableItemListField(items_types=(float,), help_text="Provean score",
required=False)
provean_converted_rankscore = fields.ListField(items_types=(float,),
provean_converted_rankscore = NullableItemListField(items_types=(float,),
help_text="Provean converted rankscore", required=False,
nullable=True)
lrt_pred = fields.ListField(items_types=(str,), help_text="LRT prediction", required=False, nullable=True)
lrt_score = fields.ListField(items_types=(float,), help_text="LRT score", required=False, nullable=True)
lrt_converted_rankscore = fields.ListField(items_types=(float,), help_text="LRT converted rankscore",
lrt_pred = NullableItemListField(items_types=(str,), help_text="LRT prediction", required=False, nullable=True)
lrt_score = NullableItemListField(items_types=(float,), help_text="LRT score", required=False, nullable=True)
lrt_converted_rankscore = NullableItemListField(items_types=(float,), help_text="LRT converted rankscore",
required=False)
lrt_omega = fields.ListField(items_types=(float,), help_text="LRT Omega", required=False, nullable=True)
cadd_raw = fields.ListField(items_types=(float,), help_text="CADD raw score", required=False, nullable=True)
cadd_raw_rankscore = fields.ListField(items_types=(float,), help_text="CADD raw rankscore",
lrt_omega = NullableItemListField(items_types=(float,), help_text="LRT Omega", required=False, nullable=True)
cadd_raw = NullableItemListField(items_types=(float,), help_text="CADD raw score", required=False, nullable=True)
cadd_raw_rankscore = NullableItemListField(items_types=(float,), help_text="CADD raw rankscore",
required=False)
cadd_phred = fields.ListField(items_types=(float,), help_text="CADD phred", required=False, nullable=True)
gm12878_confidence_value = fields.ListField(items_types=(float,),
cadd_phred = NullableItemListField(items_types=(float,), help_text="CADD phred", required=False, nullable=True)
gm12878_confidence_value = NullableItemListField(items_types=(float,),
help_text="GM12878 fitCons confidence value", required=False,
nullable=True)
gm12878_fitcons_score = fields.ListField(items_types=(float,), help_text="GM12878 fitCons score",
gm12878_fitcons_score = NullableItemListField(items_types=(float,), help_text="GM12878 fitCons score",
required=False)
gm12878_fitcons_score_rankscore = fields.ListField(items_types=(float,),
gm12878_fitcons_score_rankscore = NullableItemListField(items_types=(float,),
help_text="GM12878 fitCons rankscore", required=False,
nullable=True)
siphy_29way_logodds_rankscore = fields.ListField(items_types=(float,),
siphy_29way_logodds_rankscore = NullableItemListField(items_types=(float,),
help_text="SiPhy29way logOdds rankscore", required=False,
nullable=True)
siphy_29way_pi = fields.ListField(items_types=(float,),
siphy_29way_pi = NullableItemListField(items_types=(float,),
help_text="SiPhy29way pi", required=False, nullable=True)
phylop20way_mammalian = fields.ListField(items_types=(float,), help_text="phyloP20way mammalian",
phylop20way_mammalian = NullableItemListField(items_types=(float,), help_text="phyloP20way mammalian",
required=False)
phylop20way_mammalian_rankscore = fields.ListField(items_types=(float,),
phylop20way_mammalian_rankscore = NullableItemListField(items_types=(float,),
help_text="phyloP20way mammalian rankscore", required=False,
nullable=True)
phylop100way_vertebrate_rankscore = fields.ListField(items_types=(float,),
phylop100way_vertebrate_rankscore = NullableItemListField(items_types=(float,),
help_text="phyloP100way vertebrate rankscore", required=False,
nullable=True)
phastcons20way_mammalian = fields.ListField(items_types=(float,), help_text="phastCons20way mammalian",
phastcons20way_mammalian = NullableItemListField(items_types=(float,), help_text="phastCons20way mammalian",
required=False)
phastcons20way_mammalian_rankscore = fields.ListField(items_types=(float,),
phastcons20way_mammalian_rankscore = NullableItemListField(items_types=(float,),
help_text="phastCons20way mammalian rankscore",
required=False, nullable=True)
phastcons100way_vertebrate = fields.ListField(items_types=(float,),
phastcons100way_vertebrate = NullableItemListField(items_types=(float,),
help_text="phastCons100way vertebrate", required=False, nullable=True)
phastcons100way_vertebrate_rankscore = fields.ListField(items_types=(float,),
phastcons100way_vertebrate_rankscore = NullableItemListField(items_types=(float,),
help_text="phastCons100way vertebrate rankscore",
required=False, nullable=True)
vest3_score = fields.ListField(items_types=(float,), help_text="VEST3 score",
vest3_score = NullableItemListField(items_types=(float,), help_text="VEST3 score",
required=False)
vest3_rankscore = fields.ListField(items_types=(float,),
vest3_rankscore = NullableItemListField(items_types=(float,),
help_text="VEST3 rankscore", required=False, nullable=True)


class DBscSNV(models.Base):
version = fields.StringField(help_text="Version")
ada_score = fields.ListField(items_types=(float, ), help_text='ADA Score', required=False, nullable=True)
rf_score = fields.ListField(items_types=(float,), help_text='RF Score', required=False, nullable=True)
ada_score = NullableItemListField(items_types=(float, ), help_text='ADA Score', required=False, nullable=True)
rf_score = NullableItemListField(items_types=(float,), help_text='RF Score', required=False, nullable=True)
25 changes: 25 additions & 0 deletions varsome_api/models/fields.py
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Expand Up @@ -21,3 +21,28 @@ class DictField(fields.BaseField):

types = (dict,)


class NullableItemListField(fields.ListField):
"""
A list field that accepts None as item types
"""

def validate_single_value(self, item):
if item is None:
return
super().validate_single_value(item)

def parse_value(self, values):
"""Cast value to proper collection."""
result = self.get_default_value()

if not values:
return result

if not isinstance(values, list):
return values

return [self._cast_value(value) if value is not None else None for value in values]