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Commec Flag Rationale #92

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3 changes: 2 additions & 1 deletion commec/flag.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,8 @@ def read_flags_from_json(file_path) -> list[dict[str, str | set[str] | bool]]:
"eukaryote_flag": eukaryote_flag,
"low_concern_protein": low_concern_protein,
"low_concern_rna": low_concern_rna,
"low_concern_dna": low_concern_synbio
"low_concern_dna": low_concern_synbio,
"rationale": query.status.rationale,
})

return results
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16 changes: 8 additions & 8 deletions commec/tests/test_flag.py
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Expand Up @@ -19,14 +19,14 @@ def test_flag(tmp_path):

expected_status = textwrap.dedent(
f"""\
name,filepath,flag,biorisk,protein,nucleotide,low_concern,virus_flag,bacteria_flag,eukaryote_flag,low_concern_protein,low_concern_rna,low_concern_dna
FLAG_TEST_01,{SCREEN_DIR}/flag_tests.json,Flag,Flag,Pass,Pass,Flag,False,False,False,False,False,False
FLAG_TEST_02,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Flag,Pass,Flag,True,False,False,False,False,False
FLAG_TEST_03,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Flag,Pass,Flag,False,True,False,False,False,False
FLAG_TEST_04,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Flag,Pass,Flag,False,False,True,False,False,False
FLAG_TEST_05,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Pass,Flag,Flag,True,True,True,False,False,False
FLAG_TEST_06,{SCREEN_DIR}/flag_tests.json,Pass,Pass,Mixed,Pass,Pass,True,False,False,False,False,False
FCTEST1,{SCREEN_DIR}/functional.json,Flag,Flag,Flag,Flag,Flag,True,False,False,True,True,True
name,filepath,flag,biorisk,protein,nucleotide,low_concern,virus_flag,bacteria_flag,eukaryote_flag,low_concern_protein,low_concern_rna,low_concern_dna,rationale
FLAG_TEST_01,{SCREEN_DIR}/flag_tests.json,Flag,Flag,Pass,Pass,Flag,False,False,False,False,False,False,-
FLAG_TEST_02,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Flag,Pass,Flag,True,False,False,False,False,False,-
FLAG_TEST_03,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Flag,Pass,Flag,False,True,False,False,False,False,-
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Sorry, slow of me, but why are these rationale's -?

FLAG_TEST_04,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Flag,Pass,Flag,False,False,True,False,False,False,-
FLAG_TEST_05,{SCREEN_DIR}/flag_tests.json,Flag,Pass,Pass,Flag,Flag,True,True,True,False,False,False,-
FLAG_TEST_06,{SCREEN_DIR}/flag_tests.json,Pass,Pass,Mixed,Pass,Pass,True,False,False,False,False,False,-
FCTEST1,{SCREEN_DIR}/functional.json,Flag,Flag,Flag,Flag,Flag,True,False,False,True,True,True,"Matches sequence with pathogenic or toxin function, and protein and nucleotide sequence with regulated organisms; as well as virulence factor; as well as flags cleared as common or non-hazardous."
"""
)
actual_status = status_output.read_text()
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