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DEVSU-2990 Change header text size when adding variant text to the genomic report #120

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Merged
elewis2 merged 2 commits into from
Sep 21, 2026
Merged

DEVSU-2990 Change header text size when adding variant text to the genomic report #120

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2c59b13
- DEVSU-2990
bnguyen-bcgsc Sep 16, 2026
c47359c
- Update asserted mock variant text summary lines in test summary
bnguyen-bcgsc Sep 17, 2026
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4 changes: 2 additions & 2 deletions pori_python/ipr/summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -372,11 +372,11 @@ def prep_single_ipr_variant_comment(variant_text):
Returns:
section: html-formatted string
"""
cancer_type = ','.join(variant_text['cancerType'])
cancer_type = ', '.join(variant_text['cancerType'])
if not cancer_type:
cancer_type = 'no specific cancer types'
cancer_type = f' ({cancer_type})'
section = [f'<h2>{variant_text["variantName"]}{cancer_type}</h2>']
section = [f'<h3>{variant_text["variantName"]}{cancer_type}</h3>']
section.append(f'<p>{variant_text["text"]}</p>')
return section

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8 changes: 4 additions & 4 deletions tests/test_ipr/test_summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,7 @@ def test_gets_fully_matched_output_when_possible(self):
include_nonspecific_template=True,
)
summary_lines = ipr_summary.split('\n')
assert summary_lines[1] == '<h2>ERBB2 amplification (test1,test)</h2>'
assert summary_lines[1] == '<h3>ERBB2 amplification (test1, test)</h3>'
assert summary_lines[2] == '<p><p>normal</p></p>'
assert len(summary_lines) == 3

Expand Down Expand Up @@ -321,7 +321,7 @@ def test_includes_nonspecific_disease_matches_when_specified(self):
include_nonspecific_template=False,
)
summary_lines = ipr_summary.split('\n')
assert summary_lines[1] == '<h2>ERBB2 amplification (no specific cancer types)</h2>'
assert summary_lines[1] == '<h3>ERBB2 amplification (no specific cancer types)</h3>'
assert summary_lines[2] == '<p><p>no cancerType</p></p>'
assert len(summary_lines) == 3

Expand All @@ -340,7 +340,7 @@ def test_includes_all_graphkb_disease_matches(self):
include_nonspecific_template=False,
)
summary_lines = ipr_summary.split('\n')
assert summary_lines[1] == '<h2>ERBB2 amplification (test1,test)</h2>'
assert summary_lines[1] == '<h3>ERBB2 amplification (test1, test)</h3>'
assert summary_lines[2] == '<p><p>normal</p></p>'
assert len(summary_lines) == 3

Expand All @@ -363,7 +363,7 @@ def test_prepare_section_for_multiple_variants(self):
assert len(summary_lines) == 5
assert (
'\n'.join(summary_lines[1:])
== '<h2>ERBB2 amplification (test1,test)</h2>\n<p><p>normal</p></p>\n<h2>second variant (test1,test)</h2>\n<p><p>normal, second variant</p></p>'
== '<h3>ERBB2 amplification (test1, test)</h3>\n<p><p>normal</p></p>\n<h3>second variant (test1, test)</h3>\n<p><p>normal, second variant</p></p>'
)

def test_empty_section_when_no_variant_match(self):
Expand Down
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