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Fixed fusion related tests
1 parent d7fc5c4 commit 32ac3df

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4 files changed

+297
-60
lines changed

4 files changed

+297
-60
lines changed

portal-backend/depmap/dataset/models.py

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@@ -823,16 +823,12 @@ class Fusion(Model):
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gene_2 = relationship("Gene", foreign_keys="Fusion.gene_2_id", uselist=False)
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# New columns based on the updated schema
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profile_id = Column(String, nullable=False)
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total_reads_supporting_fusion = Column(Integer, nullable=False)
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total_fusion_coverage = Column(Integer, nullable=False)
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ffpm = Column(Float, nullable=False)
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split_reads_1 = Column(Integer, nullable=False)
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split_reads_2 = Column(Integer, nullable=False)
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discordant_mates = Column(Integer, nullable=False)
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strand1 = Column(String, nullable=False)
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strand2 = Column(String, nullable=False)
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reading_frame = Column(String, nullable=False)
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@classmethod
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def has_gene(cls, gene_id):

portal-backend/depmap/partials/data_table/factories.py

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@@ -272,31 +272,23 @@ class FusionTableSpec:
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"fusion_name",
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"gene_1_label",
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"gene_2_label",
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"profile_id",
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"total_reads_supporting_fusion",
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"total_fusion_coverage",
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"ffpm",
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"split_reads_1",
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"split_reads_2",
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"discordant_mates",
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"strand1",
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"strand2",
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"reading_frame",
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]
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common_renames = {
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"gene_1_label": "Gene 1",
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"gene_2_label": "Gene 2",
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"fusion_name": "Fusion Name",
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"profile_id": "Profile ID",
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"total_reads_supporting_fusion": "Total Reads Supporting Fusion",
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"total_fusion_coverage": "Total Fusion Coverage",
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"ffpm": "FFPM",
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"split_reads_1": "Split Reads 1",
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"split_reads_2": "Split Reads 2",
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"discordant_mates": "Discordant Mates",
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"strand1": "Strand 1",
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"strand2": "Strand 2",
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"reading_frame": "Reading Frame",
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}
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default_columns = [
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"Cell Line",

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