From 378310e7fa1dafdcee461b7d519e28eb8ad0f6fd Mon Sep 17 00:00:00 2001 From: Aaron Petkau Date: Tue, 20 Aug 2024 15:03:45 -0500 Subject: [PATCH] Fixed test samplesheet URLs --- .../data/samplesheets/samplesheet-bad-metadata_1.csv | 12 ++++++------ .../samplesheet-bad-metadata_partition.csv | 12 ++++++------ tests/data/samplesheets/samplesheet-id-mismatch.csv | 12 ++++++------ .../samplesheets/samplesheet-little-metadata.csv | 12 ++++++------ tests/data/samplesheets/samplesheet.csv | 12 ++++++------ 5 files changed, 30 insertions(+), 30 deletions(-) diff --git a/tests/data/samplesheets/samplesheet-bad-metadata_1.csv b/tests/data/samplesheets/samplesheet-bad-metadata_1.csv index 4a6bff0..2ea7d09 100644 --- a/tests/data/samplesheets/samplesheet-bad-metadata_1.csv +++ b/tests/data/samplesheets/samplesheet-bad-metadata_1.csv @@ -1,7 +1,7 @@ sample,mlst_alleles,metadata_partition,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8 -S1,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli|","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true -S2,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false -S3,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true -S4,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true -S5,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false -S6,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false +S1,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli|","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true +S2,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false +S3,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true +S4,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true +S5,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false +S6,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false diff --git a/tests/data/samplesheets/samplesheet-bad-metadata_partition.csv b/tests/data/samplesheets/samplesheet-bad-metadata_partition.csv index f8da29f..d8204c6 100644 --- a/tests/data/samplesheets/samplesheet-bad-metadata_partition.csv +++ b/tests/data/samplesheets/samplesheet-bad-metadata_partition.csv @@ -1,7 +1,7 @@ sample,mlst_alleles,metadata_partition,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8 -S1,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S1.mlst.json,1@,"Escherichia coli","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true -S2,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false -S3,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true -S4,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true -S5,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false -S6,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false +S1,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S1.mlst.json,1@,"Escherichia coli","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true +S2,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false +S3,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true +S4,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true +S5,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false +S6,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false diff --git a/tests/data/samplesheets/samplesheet-id-mismatch.csv b/tests/data/samplesheets/samplesheet-id-mismatch.csv index ee543e0..c7a7dc1 100644 --- a/tests/data/samplesheets/samplesheet-id-mismatch.csv +++ b/tests/data/samplesheets/samplesheet-id-mismatch.csv @@ -1,7 +1,7 @@ sample,mlst_alleles,metadata_partition,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8 -S1,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true -MISMATCH,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false -S3,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true -S4,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true -S5,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false -S6,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false +S1,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true +MISMATCH,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false +S3,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true +S4,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true +S5,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false +S6,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false diff --git a/tests/data/samplesheets/samplesheet-little-metadata.csv b/tests/data/samplesheets/samplesheet-little-metadata.csv index d49ce75..8831ab4 100644 --- a/tests/data/samplesheets/samplesheet-little-metadata.csv +++ b/tests/data/samplesheets/samplesheet-little-metadata.csv @@ -1,7 +1,7 @@ sample,mlst_alleles,metadata_partition,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8 -S1,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli","EHEC/STEC",,,,,, -S2,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC",,,,,, -S3,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC",,,,,, -S4,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC",,,,,, -S5,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC",,,,,, -S6,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC",,,,,, +S1,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli","EHEC/STEC",,,,,, +S2,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC",,,,,, +S3,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC",,,,,, +S4,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC",,,,,, +S5,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC",,,,,, +S6,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC",,,,,, diff --git a/tests/data/samplesheets/samplesheet.csv b/tests/data/samplesheets/samplesheet.csv index 35bf784..7e27187 100644 --- a/tests/data/samplesheets/samplesheet.csv +++ b/tests/data/samplesheets/samplesheet.csv @@ -1,7 +1,7 @@ sample,mlst_alleles,metadata_partition,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8 -S1,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true -S2,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false -S3,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true -S4,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true -S5,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false -S6,https://raw.githubusercontent.com/phac-nml/clustersplitter/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false +S1,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S1.mlst.json,1,"Escherichia coli","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true +S2,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false +S3,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true +S4,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true +S5,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false +S6,https://raw.githubusercontent.com/phac-nml/arboratornf/dev/tests/data/profiles/S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false