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Update: Include sample_name IRIDA-Next input column #23

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merged 13 commits into from
Oct 17, 2024
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Fix tests
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sgsutcliffe committed Oct 16, 2024
commit b318dc050eed34932dca437b4e1d197a81fbb677
2 changes: 1 addition & 1 deletion tests/data/metadata/expected_merged_data.tsv
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
sample sample_name outbreak organism subtype country serovar age date source special
sample_name sample outbreak organism subtype country serovar age date source special
S1 S1 1 Escherichia coli EHEC/STEC Canada O157:H7 21 2024/05/30 beef true
S2 S2 1 Escherichia coli EHEC/STEC The United States O157:H7 55 2024/05/21 milk false
S3 S3 2 Escherichia coli EPEC France O125 14 2024/04/30 cheese true
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2 changes: 1 addition & 1 deletion tests/data/metadata/little-metadata-merged.tsv
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
sample sample_name outbreak organism subtype
sample_name sample outbreak organism subtype
S1 S1 1 Escherichia coli EHEC/STEC
S2 S2 1 Escherichia coli EHEC/STEC
S3 S3 2 Escherichia coli EPEC
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2 changes: 1 addition & 1 deletion tests/data/metadata/mismatched-metadata.tsv
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
sample sample_name outbreak organism subtype country serovar age date source special
sample_name sample outbreak organism subtype country serovar age date source special
S1 S1 1 Escherichia coli EHEC/STEC Canada O157:H7 21 2024/05/30 beef true
MISMATCH MISMATCH 1 Escherichia coli EHEC/STEC The United States O157:H7 55 2024/05/21 milk false
S3 S3 2 Escherichia coli EPEC France O125 14 2024/04/30 cheese true
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12 changes: 6 additions & 6 deletions tests/data/metadata/samplenames-merged.tsv
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
sample sample_name outbreak organism subtype country serovar age date source special
S1 sample1 1 Escherichia coli EHEC/STEC Canada O157:H7 21 2024/05/30 beef true
S2 sample_2 1 Escherichia coli EHEC/STEC The United States O157:H7 55 2024/05/21 milk false
S3 sample_3 2 Escherichia coli EPEC France O125 14 2024/04/30 cheese true
S4 sample4 2 Escherichia coli EPEC France O125 35 2024/04/22 cheese true
S5 sample4_S5 3 Escherichia coli EAEC Canada O126:H27 61 2012/09/01 milk false
sample_name sample outbreak organism subtype country serovar age date source special
sample1 S1 1 Escherichia coli EHEC/STEC Canada O157:H7 21 2024/05/30 beef true
sample_2 S2 1 Escherichia coli EHEC/STEC The United States O157:H7 55 2024/05/21 milk false
sample_3 S3 2 Escherichia coli EPEC France O125 14 2024/04/30 cheese true
sample4 S4 2 Escherichia coli EPEC France O125 35 2024/04/22 cheese true
sample4_S5 S5 3 Escherichia coli EAEC Canada O126:H27 61 2012/09/01 milk false
S6 S6 unassociated Escherichia coli EAEC Canada O111:H21 43 2011/12/25 fruit false
16 changes: 8 additions & 8 deletions tests/pipelines/main.nf.test
Original file line number Diff line number Diff line change
Expand Up @@ -72,11 +72,11 @@ nextflow_pipeline {
// Check that the ArborView output is created
def actual_arborview1 = path("$launchDir/results/arborview/1_arborview.html")
assert actual_arborview1.exists()
assert actual_arborview1.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS1\\tS1\\t1\\tEscherichia coli\\tEHEC/STEC\\tCanada\\tO157:H7\\t21\\t2024/05/30\\tbeef\\tTrue\\nS2\\tS2\\t1\\tEscherichia coli\\tEHEC/STEC\\tThe United States\\tO157:H7\\t55\\t2024/05/21\\tmilk\\tFalse\\n")
assert actual_arborview1.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS1\\tS1\\t1\\tEscherichia coli\\tEHEC/STEC\\tCanada\\tO157:H7\\t21\\t2024/05/30\\tbeef\\tTrue\\nS2\\tS2\\t1\\tEscherichia coli\\tEHEC/STEC\\tThe United States\\tO157:H7\\t55\\t2024/05/21\\tmilk\\tFalse\\n")

def actual_arborview2 = path("$launchDir/results/arborview/2_arborview.html")
assert actual_arborview2.exists()
assert actual_arborview2.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS3\\tS3\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t14\\t2024/04/30\\tcheese\\tTrue\\nS4\\tS4\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t35\\t2024/04/22\\tcheese\\tTrue\\n")
assert actual_arborview2.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS3\\tS3\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t14\\t2024/04/30\\tcheese\\tTrue\\nS4\\tS4\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t35\\t2024/04/22\\tcheese\\tTrue\\n")

// compare IRIDA Next JSON output
def iridanext_json = path("$launchDir/results/iridanext.output.json").json
Expand Down Expand Up @@ -179,11 +179,11 @@ nextflow_pipeline {
// Check that the ArborView output is created
def actual_arborview1 = path("$launchDir/results/arborview/1_arborview.html")
assert actual_arborview1.exists()
assert actual_arborview1.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\nS1\\tS1\\t1\\tEscherichia coli\\tEHEC/STEC\\nS2\\tS2\\t1\\tEscherichia coli\\tEHEC/STEC\\n")
assert actual_arborview1.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\nS1\\tS1\\t1\\tEscherichia coli\\tEHEC/STEC\\nS2\\tS2\\t1\\tEscherichia coli\\tEHEC/STEC\\n")

def actual_arborview2 = path("$launchDir/results/arborview/2_arborview.html")
assert actual_arborview2.exists()
assert actual_arborview2.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\nS3\\tS3\\t2\\tEscherichia coli\\tEPEC\\nS4\\tS4\\t2\\tEscherichia coli\\tEPEC\\n")
assert actual_arborview2.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\nS3\\tS3\\t2\\tEscherichia coli\\tEPEC\\nS4\\tS4\\t2\\tEscherichia coli\\tEPEC\\n")

// compare IRIDA Next JSON output
def iridanext_json = path("$launchDir/results/iridanext.output.json").json
Expand Down Expand Up @@ -437,11 +437,11 @@ nextflow_pipeline {
// Check that the ArborView output is created
def actual_arborview1 = path("$launchDir/results/arborview/1_arborview.html")
assert actual_arborview1.exists()
assert actual_arborview1.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS1\\tS1\\t1\\tEscherichia coli\\tEHEC/STEC\\tCanada\\tO157:H7\\t21\\t2024/05/30\\tbeef\\tTrue\\nMISMATCH\\tMISMATCH\\t1\\tEscherichia coli\\tEHEC/STEC\\tThe United States\\tO157:H7\\t55\\t2024/05/21\\tmilk\\tFalse\\n")
assert actual_arborview1.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS1\\tS1\\t1\\tEscherichia coli\\tEHEC/STEC\\tCanada\\tO157:H7\\t21\\t2024/05/30\\tbeef\\tTrue\\nMISMATCH\\tMISMATCH\\t1\\tEscherichia coli\\tEHEC/STEC\\tThe United States\\tO157:H7\\t55\\t2024/05/21\\tmilk\\tFalse\\n")

def actual_arborview2 = path("$launchDir/results/arborview/2_arborview.html")
assert actual_arborview2.exists()
assert actual_arborview2.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS3\\tS3\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t14\\t2024/04/30\\tcheese\\tTrue\\nS4\\tS4\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t35\\t2024/04/22\\tcheese\\tTrue\\n")
assert actual_arborview2.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS3\\tS3\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t14\\t2024/04/30\\tcheese\\tTrue\\nS4\\tS4\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t35\\t2024/04/22\\tcheese\\tTrue\\n")

// compare IRIDA Next JSON output
def iridanext_json = path("$launchDir/results/iridanext.output.json").json
Expand Down Expand Up @@ -544,11 +544,11 @@ nextflow_pipeline {
// Check that the ArborView output is created
def actual_arborview1 = path("$launchDir/results/arborview/1_arborview.html")
assert actual_arborview1.exists()
assert actual_arborview1.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS1\\tsample1\\t1\\tEscherichia coli\\tEHEC/STEC\\tCanada\\tO157:H7\\t21\\t2024/05/30\\tbeef\\tTrue\\nS2\\tsample_2\\t1\\tEscherichia coli\\tEHEC/STEC\\tThe United States\\tO157:H7\\t55\\t2024/05/21\\tmilk\\tFalse\\n")
assert actual_arborview1.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nsample1\\tS1\\t1\\tEscherichia coli\\tEHEC/STEC\\tCanada\\tO157:H7\\t21\\t2024/05/30\\tbeef\\tTrue\\nsample_2\\tS2\\t1\\tEscherichia coli\\tEHEC/STEC\\tThe United States\\tO157:H7\\t55\\t2024/05/21\\tmilk\\tFalse\\n")

def actual_arborview2 = path("$launchDir/results/arborview/2_arborview.html")
assert actual_arborview2.exists()
assert actual_arborview2.text.contains("sample\\tsample_name\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nS3\\tsample_3\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t14\\t2024/04/30\\tcheese\\tTrue\\nS4\\tsample4\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t35\\t2024/04/22\\tcheese\\tTrue\\n")
assert actual_arborview2.text.contains("sample_name\\tsample\\toutbreak\\torganism\\tsubtype\\tcountry\\tserovar\\tage\\tdate\\tsource\\tspecial\\nsample_3\\tS3\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t14\\t2024/04/30\\tcheese\\tTrue\\nsample4\\tS4\\t2\\tEscherichia coli\\tEPEC\\tFrance\\tO125\\t35\\t2024/04/22\\tcheese\\tTrue\\n")

// compare IRIDA Next JSON output
def iridanext_json = path("$launchDir/results/iridanext.output.json").json
Expand Down
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