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Allow filtering variant experiment by sample #1399

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merged 3 commits into from
Dec 6, 2024
Merged

Allow filtering variant experiment by sample #1399

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90eaabb
Fix remove the deprecated option
gregorjerse Nov 26, 2024
da08199
Remove deprecated isort option
gregorjerse Dec 2, 2024
eeb0a15
Allow filtering variant experiment by sample
gregorjerse Nov 11, 2024
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14 changes: 10 additions & 4 deletions docs/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,16 @@ All notable changes to this project are documented in this file.
This project adheres to `Semantic Versioning <http://semver.org/>`_.


==========
Unreleased
==========

Added
-----
- Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
- Use generic permission filters when filtering variants by related models


===================
61.0.0 - 2024-11-21
===================
Expand All @@ -20,10 +30,6 @@ Changed
60.0.0 - 2024-11-19
===================

Added
-----
- Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 41.x
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2 changes: 1 addition & 1 deletion resolwe_bio/processes/import_data/geneset.py
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Expand Up @@ -18,7 +18,7 @@

def parse_geneset_file(geneset_file, warning):
"""Parse geneset file."""
with open(geneset_file, "rU") as handle:
with open(geneset_file, "r") as handle:
# skip empty lines
genes = [str(line.strip()) for line in handle if line.strip()]
geneset = sorted(set(genes))
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90 changes: 41 additions & 49 deletions resolwe_bio/variants/filters.py
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Expand Up @@ -6,14 +6,14 @@

"""

import django_filters as filters

from resolwe.flow.filters import (
DATETIME_LOOKUPS,
NUMBER_LOOKUPS,
RELATED_LOOKUPS,
TEXT_LOOKUPS,
CheckQueryParamsMixin,
BaseResolweFilter,
DataFilter,
FilterRelatedWithPermissions,
)

from resolwe_bio.variants.models import (
Expand All @@ -24,9 +24,42 @@
)


class VariantFilter(CheckQueryParamsMixin, filters.FilterSet):
class VariantCallFilter(BaseResolweFilter):
"""Filter the VariantCall objects endpoint."""

data = FilterRelatedWithPermissions(DataFilter)

class Meta:
"""Filter configuration."""

model = VariantCall
fields = {
"id": NUMBER_LOOKUPS,
"sample__slug": TEXT_LOOKUPS,
"sample": RELATED_LOOKUPS,
"variant": RELATED_LOOKUPS,
"variant__species": TEXT_LOOKUPS,
"variant__genome_assembly": TEXT_LOOKUPS,
"variant__chromosome": TEXT_LOOKUPS,
"variant__position": NUMBER_LOOKUPS,
"variant__reference": TEXT_LOOKUPS,
"variant__alternative": TEXT_LOOKUPS,
"experiment": RELATED_LOOKUPS,
"quality": NUMBER_LOOKUPS,
"depth": NUMBER_LOOKUPS,
"filter": TEXT_LOOKUPS,
"genotype": TEXT_LOOKUPS,
"genotype_quality": NUMBER_LOOKUPS,
"alternative_allele_depth": NUMBER_LOOKUPS,
"depth_norm_quality": NUMBER_LOOKUPS,
}


class VariantFilter(BaseResolweFilter):
"""Filter the Variant objects endpoint."""

variant_calls = FilterRelatedWithPermissions(VariantCallFilter)

class Meta:
"""Filter configuration."""

Expand All @@ -51,18 +84,6 @@ class Meta:
"annotation__clinical_significance": TEXT_LOOKUPS,
"annotation__dbsnp_id": TEXT_LOOKUPS,
"annotation__clinvar_id": TEXT_LOOKUPS,
"annotation__data": RELATED_LOOKUPS,
"variant_calls": RELATED_LOOKUPS,
"variant_calls__quality": NUMBER_LOOKUPS,
"variant_calls__depth": NUMBER_LOOKUPS,
"variant_calls__sample__slug": TEXT_LOOKUPS,
"variant_calls__sample": RELATED_LOOKUPS,
"variant_calls__experiment": RELATED_LOOKUPS,
"variant_calls__filter": TEXT_LOOKUPS,
"variant_calls__genotype": TEXT_LOOKUPS,
"variant_calls__genotype_quality": NUMBER_LOOKUPS,
"variant_calls__alternative_allele_depth": NUMBER_LOOKUPS,
"variant_calls__depth_norm_quality": NUMBER_LOOKUPS,
}

@property
Expand All @@ -72,7 +93,7 @@ def qs(self):
return parent.distinct()


class VariantAnnotationFilter(CheckQueryParamsMixin, filters.FilterSet):
class VariantAnnotationFilter(BaseResolweFilter):
"""Filter the VariantAnnotation objects endpoint."""

class Meta:
Expand All @@ -94,40 +115,11 @@ class Meta:
}


class VariantCallFilter(CheckQueryParamsMixin, filters.FilterSet):
"""Filter the VariantCall objects endpoint."""

class Meta:
"""Filter configuration."""

model = VariantCall
fields = {
"id": NUMBER_LOOKUPS,
"sample__slug": TEXT_LOOKUPS,
"sample": RELATED_LOOKUPS,
"data__slug": TEXT_LOOKUPS,
"data": RELATED_LOOKUPS,
"variant": RELATED_LOOKUPS,
"variant__species": TEXT_LOOKUPS,
"variant__genome_assembly": TEXT_LOOKUPS,
"variant__chromosome": TEXT_LOOKUPS,
"variant__position": NUMBER_LOOKUPS,
"variant__reference": TEXT_LOOKUPS,
"variant__alternative": TEXT_LOOKUPS,
"experiment": RELATED_LOOKUPS,
"quality": NUMBER_LOOKUPS,
"depth": NUMBER_LOOKUPS,
"filter": TEXT_LOOKUPS,
"genotype": TEXT_LOOKUPS,
"genotype_quality": NUMBER_LOOKUPS,
"alternative_allele_depth": NUMBER_LOOKUPS,
"depth_norm_quality": NUMBER_LOOKUPS,
}


class VariantExperimentFilter(CheckQueryParamsMixin, filters.FilterSet):
class VariantExperimentFilter(BaseResolweFilter):
"""Filter the VariantExperiment objects endpoint."""

variant_calls = FilterRelatedWithPermissions(VariantCallFilter)

class Meta:
"""Filter configuration."""

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