Release/v1.0.0

[mathieulemieux]

Breaking Changes

• [KBDEV-1227] Signature variants support #42
• [DEVSU-2550, DEVSU-2477] Multivariant statements handling #45, #37

Improvements

• [KBDEV-1236] Added extra type checking for variant matching #25
• [DEVSU-2488] Move reformatting upstream get_cancer_predisposition_info() #41
• [DEVSU-2494] Add custom text to analysis summary #44, #46
• [SDEV-4409] Deprecate get_cancer_predisposition_info() & get_pharmacogenomic_info() #35
• Add image to test_upload contents #48

Bugfixes

• [KBDEV-1266] Fix redundand disease matching #47
• [SDEV-4605, SDEV-4601] Remove pattern check on chromosomeBand #43
• [DEVSU-2606], Combine chr with chromosomeBand #53

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 85.01742% with 43 lines in your changes missing coverage. Please review.

Project coverage is 86.14%. Comparing base (3a7392b) to head (a9e1e27).

Files with missing lines	Patch %	Lines
pori_python/ipr/ipr.py	73.23%	19 Missing ⚠️
pori_python/ipr/annotate.py	47.36%	10 Missing ⚠️
pori_python/graphkb/match.py	72.41%	8 Missing ⚠️
pori_python/ipr/main.py	87.17%	5 Missing ⚠️
pori_python/ipr/inputs.py	97.67%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #49      +/-   ##
==========================================
- Coverage   86.23%   86.14%   -0.09%     
==========================================
  Files          18       18              
  Lines        2157     2410     +253     
==========================================
+ Hits         1860     2076     +216     
- Misses        297      334      +37     

Flag	Coverage Δ
unittests	86.14% <85.01%> (-0.09%)	⬇️

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[mathieulemieux]

Flagging "Signature variants support" & "Multivariant statements handling" as breaking changes since it's breaking in regards to the IPR API.

[mathieulemieux]

Running the gsc_report test suit, I'm getting one error: ValueError: Missing required IPR Expression column: ['kbCategory'].

@dustinbleile , do you think it's something that need to be fixed on the pori_python side or on gsc_report?

========================================================================== FAILURES ==========================================================================
____________________________________________ TestExpression.test_expression_categories_from_microservice_average _____________________________________________

self = <test_expression_categories.TestExpression object at 0x7f39c2f61010>

    @pytest.mark.skipif("bamboo" in os.getcwd(), reason="Bamboo has no vardbmicro access")
    def test_expression_categories_from_microservice_average(self):
>       exp = vdb_expression_categories(
            expression_file=HNSC_EXP_INPUT["expression_file"],
            disease_expression_comp_list=["average"],
            gtex_comps=["average", "skeletal_muscle"],
            genes=HNSC_EXP_INPUT["genes"],
            val_column="targetExp",
            gene_col_name="hugo",
            ipr_columns_only=True,
            val_units="rpkm",
        )

tests/genome_process/measures/test_expression_categories.py:250: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
gsc_report/genome_process/measures/expression_categories.py:880: in vdb_expression_categories
    exp = ipr_columns(exp)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

exp =      hugo PTX_Accession PTX_hugo  PTX_Abundance  ...  biopsySitekIQR  biopsySite_percent_zeroes  biopsySitePercentile ...     NaN  ...            -1.8                        0.0                   0.0               NaN

[2 rows x 85 columns]
gene_col = '', max_errors = 200

    def ipr_columns(exp: pd.DataFrame, gene_col: str = "", max_errors: int = 200) -> pd.DataFrame:
        f"""Only columns {EXP_REQ} and optionally {EXP_OPTIONAL} and {ENSEMBL_COLS}
    
        Args:
            gene_col(str): column name to use for GraphKB gene matching and IPR display / joining.
                           by default IPR assumes the name 'gene'
    
        """
        alt_gene_cols = [col for col in GENE_COLS if col in exp.columns]
        if gene_col:
            exp.rename(columns={gene_col: "gene"})
        elif "gene" not in exp.columns and alt_gene_cols:
            logger.warning(f"ipr_columns assuming {alt_gene_cols} for 'gene'")
            exp.rename(columns={gene_col: alt_gene_cols[0]})
    
        missing_reqs = [col for col in EXP_REQ if col not in exp.columns]
        if missing_reqs:
>           raise ValueError(f"Missing required IPR Expression column: {missing_reqs}")
E           ValueError: Missing required IPR Expression column: ['kbCategory']

gsc_report/genome_process/measures/expression.py:138: ValueError

[mathieulemieux]

Having the exact same error with both main and current release branch...

[dustinbleile]

@mathieulemieux I could not reproduce gsc_report errors.
My tests ran.
Looks like your failures are unrelated to pori_python and might have to do with access to the pediatric test_data at the gsc.

[mathieulemieux]

@mathieulemieux I could not reproduce gsc_report errors. My tests ran. Looks like your failures are unrelated to pori_python and might have to do with access to the pediatric test_data at the gsc.

Ok, I'm glad to hear that. I have the peds_pog & PROFYLE_dart groups but maybe I'm missing one. Anyway, I'm happy enough with you having the tests passing!