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Renamed fields for API's variantdata requests #137

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merged 7 commits into from
Oct 17, 2024
Merged

Renamed fields for API's variantdata requests #137

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25d1792
Changed dict structure for variantdata api requests
Shettland Oct 2, 2024
d3ac1c3
Informative message when there is no data to be shown
Shettland Oct 2, 2024
771a358
Adapted some dict keys to long_table fields
Shettland Oct 3, 2024
7b9c37f
Included more options to select time period to lineages VOC
Shettland Oct 3, 2024
89ab1d8
fixed filter key for variant data
Shettland Oct 15, 2024
bf98a21
Renamed keys for variant data. linting
Shettland Oct 15, 2024
2214335
Increased time options for lineage graph
Shettland Oct 15, 2024
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22 changes: 13 additions & 9 deletions core/api/utils/variants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ def create_or_get_filter_obj(filter_value):
if core.models.Filter.objects.filter(filter__iexact=filter_value).exists():
return core.models.Filter.objects.filter(filter__iexact=filter_value).last()
filter_serializer = core.api.serializers.CreateFilterSerializer(
data={"filter": filter_value}
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I'd prefer this in low case, is it possible?

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Maybe we can apply lowercase to all the fields prior to sending the request

data={"Filter": filter_value}
)
if filter_serializer.is_valid():
filter_obj = filter_serializer.save()
Expand Down Expand Up @@ -62,13 +62,13 @@ def store_variant_in_sample(v_data):

def get_variant_id(data):
"""look out for the necessary reference ids to create the variance instance"""
chr_obj = core.utils.variants.get_if_chromosomes_exists(data["Chromosome"])
chr_obj = core.utils.variants.get_if_chromosomes_exists(data["chromosome"])
if chr_obj is None:
return {"ERROR": core.config.ERROR_CHROMOSOME_NOT_DEFINED_IN_DATABASE}
variant_obj = core.models.Variant.objects.filter(
chromosomeID_id=chr_obj,
pos__iexact=data["Variant"]["pos"],
alt__iexact=data["Variant"]["alt"],
pos__iexact=data["pos"],
alt__iexact=data["alt"],
).last()
if variant_obj is None:
# Create the variant
Expand All @@ -78,9 +78,9 @@ def get_variant_id(data):
variant_dict = {}
variant_dict["chromosomeID_id"] = chr_obj.get_chromosome_id()
variant_dict["filterID_id"] = filter_obj.get_filter_id()
variant_dict["pos"] = data["Variant"]["pos"]
variant_dict["alt"] = data["Variant"]["alt"]
variant_dict["ref"] = data["Variant"]["ref"]
variant_dict["pos"] = data["pos"]
variant_dict["alt"] = data["alt"]
variant_dict["ref"] = data["ref"]
variant_serializer = core.api.serializers.CreateVariantSerializer(
data=variant_dict
)
Expand All @@ -99,12 +99,12 @@ def get_variant_analysis_defined(s_obj):
def get_required_variant_ann_id(data):
"""Look for the ids that variant annotation needs"""
v_ann_ids = {}
gene_obj = core.utils.variants.get_gene_obj_from_gene_name(data["Gene"])
gene_obj = core.utils.variants.get_gene_obj_from_gene_name(data["gene"])

if gene_obj is None:
return {"ERROR": core.config.ERROR_GENE_NOT_DEFINED_IN_DATABASE}
v_ann_ids["geneID_id"] = gene_obj.get_gene_id()
effect_obj = create_or_get_effect_obj(data["Effect"])
effect_obj = create_or_get_effect_obj(data["effect"])
if isinstance(effect_obj, dict):
return effect_obj
v_ann_ids["geneID_id"] = gene_obj.get_gene_id()
Expand All @@ -122,6 +122,8 @@ def split_variant_data(data, sample_obj, date):
split_data["variant_in_sample"]["variantID_id"] = variant_id
split_data["variant_in_sample"]["analysis_date"] = date

var_keys = ["dp", "ref_dp", "alt_dp", "af"]
data["VariantInSample"] = {x: y for x, y in data.items() if x in var_keys}
split_data["variant_in_sample"].update(data["VariantInSample"])

v_ann_id = get_required_variant_ann_id(data)
Expand All @@ -130,6 +132,8 @@ def split_variant_data(data, sample_obj, date):
split_data["variant_ann"] = v_ann_id
split_data["variant_ann"]["variantID_id"] = variant_id

annot_keys = ["hgvs_c", "hgvs_p", "hgvs_p_1_letter"]
data["VariantAnnotation"] = {x: y for x, y in data.items() if x in annot_keys}
split_data["variant_ann"].update(data["VariantAnnotation"])
return split_data

Expand Down
2 changes: 2 additions & 0 deletions core/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -258,6 +258,8 @@ def intranet(request):
intra_data["ena_graph"] = core.utils.public_db.percentage_graphic(
len(sample_lab_objs), len(ena_acc), ""
)
else:
intra_data = f"No samples found for selected laboratory: {lab_name}"
return render(request, "core/intranet.html", {"intra_data": intra_data})
else:
# loged user belongs to Relecov Manager group
Expand Down
4 changes: 4 additions & 0 deletions dashboard/utils/var_lineage_variation_over_time_graph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,13 @@ def create_lineages_variations_graphic(date_range=None):
id="periodTime",
options=[
{"label": "Select Period", "value": ""},
{"label": "Last 4 years", "value": "1460"},
{"label": "Last 2 years", "value": "730"},
{"label": "Last year", "value": "365"},
{"label": "Last 6 months", "value": "180"},
{"label": "Last 3 months", "value": "90"},
{"label": "Last month", "value": "30"},
{"label": "Last week", "value": "7"},
],
),
],
Expand Down
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