From cbc65acf2ddcfa73485a9804c7afe7cb6dea9634 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Mon, 1 Oct 2018 11:44:01 -0500 Subject: [PATCH] need to keep exact MiAIRR field name --- lang/R/inst/extdata/airr-schema.yaml | 2 +- lang/python/airr/specs/airr-schema.yaml | 2 +- lang/python/examples/florian.airr.yaml | 120 +++++++++--------- lang/python/examples/query1-1_repertoire.json | 2 +- lang/python/examples/query1-2_repertoire.json | 2 +- lang/python/examples/query1-3_repertoire.json | 2 +- lang/python/examples/query1-4_repertoire.json | 2 +- lang/python/examples/query1_repertoire.json | 2 +- lang/python/examples/query2_repertoire.json | 2 +- specs/airr-schema.yaml | 2 +- 10 files changed, 69 insertions(+), 69 deletions(-) diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index 87264ae91..2d4680699 100644 --- a/lang/R/inst/extdata/airr-schema.yaml +++ b/lang/R/inst/extdata/airr-schema.yaml @@ -254,7 +254,7 @@ PCRTarget: discriminator: AIRR type: object properties: - locus: + pcr_target_locus: type: string description: Designation of the target locus according to standard gene nomencleature x-miairr: true diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index 87264ae91..2d4680699 100644 --- a/lang/python/airr/specs/airr-schema.yaml +++ b/lang/python/airr/specs/airr-schema.yaml @@ -254,7 +254,7 @@ PCRTarget: discriminator: AIRR type: object properties: - locus: + pcr_target_locus: type: string description: Designation of the target locus according to standard gene nomencleature x-miairr: true diff --git a/lang/python/examples/florian.airr.yaml b/lang/python/examples/florian.airr.yaml index 823ca9da7..3fe1fd1ba 100644 --- a/lang/python/examples/florian.airr.yaml +++ b/lang/python/examples/florian.airr.yaml @@ -43,7 +43,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -84,7 +84,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -125,7 +125,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -166,7 +166,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -207,7 +207,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -248,7 +248,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -289,7 +289,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -330,7 +330,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -371,7 +371,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -412,7 +412,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -453,7 +453,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -494,7 +494,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -535,7 +535,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -576,7 +576,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -617,7 +617,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -658,7 +658,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -699,7 +699,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -740,7 +740,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -781,7 +781,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -822,7 +822,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -863,7 +863,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -904,7 +904,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -945,7 +945,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -986,7 +986,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1027,7 +1027,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1068,7 +1068,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1109,7 +1109,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1150,7 +1150,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1191,7 +1191,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1232,7 +1232,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1273,7 +1273,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1314,7 +1314,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1355,7 +1355,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1396,7 +1396,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1437,7 +1437,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1478,7 +1478,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1519,7 +1519,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1560,7 +1560,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1601,7 +1601,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1642,7 +1642,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1683,7 +1683,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1724,7 +1724,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1765,7 +1765,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1806,7 +1806,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1847,7 +1847,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1888,7 +1888,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1929,7 +1929,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -1970,7 +1970,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2011,7 +2011,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2052,7 +2052,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2093,7 +2093,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2134,7 +2134,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2175,7 +2175,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2216,7 +2216,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2257,7 +2257,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2298,7 +2298,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: IGH + - pcr_target_locus: IGH sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2339,7 +2339,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2380,7 +2380,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2421,7 +2421,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq @@ -2462,7 +2462,7 @@ Repertoire: cell_isolation: FACS template_class: RNA pcr_target: - - locus: TRB + - pcr_target_locus: TRB sequencing_platform: "Illumina MiSeq" read_length: "300" file_type: fastq diff --git a/lang/python/examples/query1-1_repertoire.json b/lang/python/examples/query1-1_repertoire.json index 007c03683..6dec2a488 100644 --- a/lang/python/examples/query1-1_repertoire.json +++ b/lang/python/examples/query1-1_repertoire.json @@ -12,7 +12,7 @@ { "op":"=", "content": { - "field":"sample.pcr_target.locus", + "field":"sample.pcr_target.pcr_target_locus", "value":"TRB" } } diff --git a/lang/python/examples/query1-2_repertoire.json b/lang/python/examples/query1-2_repertoire.json index d198e569d..42b402784 100644 --- a/lang/python/examples/query1-2_repertoire.json +++ b/lang/python/examples/query1-2_repertoire.json @@ -12,7 +12,7 @@ { "op":"=", "content": { - "field":"sample.pcr_target.locus", + "field":"sample.pcr_target.pcr_target_locus", "value":"TRB" } } diff --git a/lang/python/examples/query1-3_repertoire.json b/lang/python/examples/query1-3_repertoire.json index ab2537026..f352405bf 100644 --- a/lang/python/examples/query1-3_repertoire.json +++ b/lang/python/examples/query1-3_repertoire.json @@ -1,3 +1,3 @@ { - "facets":"sample.pcr_target.locus" + "facets":"sample.pcr_target.pcr_target_locus" } diff --git a/lang/python/examples/query1-4_repertoire.json b/lang/python/examples/query1-4_repertoire.json index 93d9cc08f..d67aed064 100644 --- a/lang/python/examples/query1-4_repertoire.json +++ b/lang/python/examples/query1-4_repertoire.json @@ -2,7 +2,7 @@ "filters":{ "op":"=", "content": { - "field":"sample.pcr_target.locus", + "field":"sample.pcr_target.pcr_target_locus", "value":"IGH" } }, diff --git a/lang/python/examples/query1_repertoire.json b/lang/python/examples/query1_repertoire.json index 004696b5f..d88da6a1c 100644 --- a/lang/python/examples/query1_repertoire.json +++ b/lang/python/examples/query1_repertoire.json @@ -12,7 +12,7 @@ { "op":"=", "content": { - "field":"sample.pcr_target.locus", + "field":"sample.pcr_target.pcr_target_locus", "value":"TRB" } } diff --git a/lang/python/examples/query2_repertoire.json b/lang/python/examples/query2_repertoire.json index 3ea9a425c..16ca08dc0 100644 --- a/lang/python/examples/query2_repertoire.json +++ b/lang/python/examples/query2_repertoire.json @@ -12,7 +12,7 @@ { "op":"=", "content": { - "field":"sample.pcr_target.locus", + "field":"sample.pcr_target.pcr_target_locus", "value":"IGH" } }, diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index 87264ae91..2d4680699 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -254,7 +254,7 @@ PCRTarget: discriminator: AIRR type: object properties: - locus: + pcr_target_locus: type: string description: Designation of the target locus according to standard gene nomencleature x-miairr: true