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feat: added amino acid insertion search, added many test cases and fi…
…xed various bugs
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40 changes: 40 additions & 0 deletions
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endToEndTests/test/queries/aaInsertionsActionOneSequence.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,40 @@ | ||
{ | ||
"testCaseName": "amino acid insertions action only one sequence", | ||
"query": { | ||
"action": { | ||
"type": "AminoAcidInsertions", | ||
"column": "aaInsertions", | ||
"orderByFields": ["insertions", "position"], | ||
"sequenceName": "S" | ||
}, | ||
"filterExpression": { | ||
"type": "True" | ||
} | ||
}, | ||
"expectedQueryResult": [ | ||
{ | ||
"count": 5, | ||
"insertions": "EPE", | ||
"position": 214, | ||
"sequenceName": "S" | ||
}, | ||
{ | ||
"count": 1, | ||
"insertions": "IV", | ||
"position": 210, | ||
"sequenceName": "S" | ||
}, | ||
{ | ||
"count": 1, | ||
"insertions": "SGE", | ||
"position": 247, | ||
"sequenceName": "S" | ||
}, | ||
{ | ||
"count": 1, | ||
"insertions": "T", | ||
"position": 143, | ||
"sequenceName": "S" | ||
} | ||
] | ||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,39 @@ | ||
{ | ||
"testCaseName": "amino acid insertions contains filter", | ||
"query": { | ||
"action": { | ||
"type": "Details", | ||
"fields": ["aaInsertions", "gisaid_epi_isl"], | ||
"orderByFields": ["gisaid_epi_isl"] | ||
}, | ||
"filterExpression": { | ||
"type": "AminoAcidInsertionContains", | ||
"sequenceName": "S", | ||
"value": "E.*E", | ||
"column": "aaInsertions", | ||
"position": 214 | ||
} | ||
}, | ||
"expectedQueryResult": [ | ||
{ | ||
"aaInsertions": "S:214:EPE", | ||
"gisaid_epi_isl": "EPI_ISL_1003629" | ||
}, | ||
{ | ||
"aaInsertions": "S:214:EPE", | ||
"gisaid_epi_isl": "EPI_ISL_1408408" | ||
}, | ||
{ | ||
"aaInsertions": "S:214:EPE", | ||
"gisaid_epi_isl": "EPI_ISL_1597932" | ||
}, | ||
{ | ||
"aaInsertions": "S:214:EPE", | ||
"gisaid_epi_isl": "EPI_ISL_1750868" | ||
}, | ||
{ | ||
"aaInsertions": "S:214:EPE", | ||
"gisaid_epi_isl": "EPI_ISL_581968" | ||
} | ||
] | ||
} |
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