diff --git a/ena_upload/templates/ENA_template_PLATFORM.xml b/ena_upload/templates/ENA_template_PLATFORM.xml index 8ba2974..b4802f0 100644 --- a/ena_upload/templates/ENA_template_PLATFORM.xml +++ b/ena_upload/templates/ENA_template_PLATFORM.xml @@ -26,6 +26,7 @@ Illumina MiSeq Illumina MiniSeq Illumina NovaSeq X + Illumina NovaSeq X Plus Illumina NovaSeq 6000 NextSeq 500 NextSeq 550 @@ -101,6 +102,7 @@ DNBSEQ-G400 DNBSEQ-G50 DNBSEQ-G400 FAST + DNBSEQ-T10x4RS unspecified diff --git a/ena_upload/templates/ENA_template_samples_ERC000011.xml b/ena_upload/templates/ENA_template_samples_ERC000011.xml index 0eba21f..96ac3b8 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000011.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000011.xml @@ -87,12 +87,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (region and locality) @@ -123,6 +117,12 @@ def mandatorytest(row, column, index): ${row['sex']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + lab_host diff --git a/ena_upload/templates/ENA_template_samples_ERC000012.xml b/ena_upload/templates/ENA_template_samples_ERC000012.xml index 6d8f3d4..cf940a7 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000012.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000012.xml @@ -179,12 +179,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -262,6 +256,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000013.xml b/ena_upload/templates/ENA_template_samples_ERC000013.xml index a52c525..94c8617 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000013.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000013.xml @@ -203,12 +203,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -285,6 +279,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000014.xml b/ena_upload/templates/ENA_template_samples_ERC000014.xml index a058565..21d2520 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000014.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000014.xml @@ -203,12 +203,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -273,6 +267,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + nose/mouth/teeth/throat disorder diff --git a/ena_upload/templates/ENA_template_samples_ERC000015.xml b/ena_upload/templates/ENA_template_samples_ERC000015.xml index 68919a3..785c903 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000015.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000015.xml @@ -191,12 +191,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -261,6 +255,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + gastrointestinal tract disorder diff --git a/ena_upload/templates/ENA_template_samples_ERC000016.xml b/ena_upload/templates/ENA_template_samples_ERC000016.xml index d8979e9..089b235 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000016.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000016.xml @@ -197,12 +197,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -267,6 +261,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + nose/mouth/teeth/throat disorder diff --git a/ena_upload/templates/ENA_template_samples_ERC000017.xml b/ena_upload/templates/ENA_template_samples_ERC000017.xml index b9c1a8e..c18d09c 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000017.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000017.xml @@ -191,12 +191,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -261,6 +255,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + dermatology disorder diff --git a/ena_upload/templates/ENA_template_samples_ERC000018.xml b/ena_upload/templates/ENA_template_samples_ERC000018.xml index 6fa9752..9e27baf 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000018.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000018.xml @@ -191,12 +191,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -261,6 +255,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + gynecological disorder diff --git a/ena_upload/templates/ENA_template_samples_ERC000019.xml b/ena_upload/templates/ENA_template_samples_ERC000019.xml index 5f1a08e..fbc9d0a 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000019.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000019.xml @@ -179,12 +179,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -256,6 +250,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000020.xml b/ena_upload/templates/ENA_template_samples_ERC000020.xml index 68e6842..6739699 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000020.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000020.xml @@ -203,12 +203,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -297,6 +291,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000021.xml b/ena_upload/templates/ENA_template_samples_ERC000021.xml index 89cd672..d9b0d3b 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000021.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000021.xml @@ -198,12 +198,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -275,6 +269,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000022.xml b/ena_upload/templates/ENA_template_samples_ERC000022.xml index 1618ac6..de72141 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000022.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000022.xml @@ -216,12 +216,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -317,6 +311,12 @@ def mandatorytest(row, column, index): ${row['extreme_unusual_properties/Al saturation method']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000023.xml b/ena_upload/templates/ENA_template_samples_ERC000023.xml index ed8f8b0..4b146b4 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000023.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000023.xml @@ -179,12 +179,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -249,6 +243,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + biochemical oxygen demand diff --git a/ena_upload/templates/ENA_template_samples_ERC000024.xml b/ena_upload/templates/ENA_template_samples_ERC000024.xml index 13219ee..ac73cca 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000024.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000024.xml @@ -200,12 +200,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -277,6 +271,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000025.xml b/ena_upload/templates/ENA_template_samples_ERC000025.xml index 8f8ebd1..de5b782 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000025.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000025.xml @@ -186,12 +186,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -263,6 +257,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000027.xml b/ena_upload/templates/ENA_template_samples_ERC000027.xml index adbff3b..2d3727c 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000027.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000027.xml @@ -219,12 +219,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - broad-scale environmental context @@ -300,6 +294,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + specific host diff --git a/ena_upload/templates/ENA_template_samples_ERC000028.xml b/ena_upload/templates/ENA_template_samples_ERC000028.xml index dad6a27..a202000 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000028.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000028.xml @@ -57,12 +57,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (region and locality) @@ -87,6 +81,12 @@ def mandatorytest(row, column, index): ${row['mating_type']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host health state diff --git a/ena_upload/templates/ENA_template_samples_ERC000029.xml b/ena_upload/templates/ENA_template_samples_ERC000029.xml index 990525e..033fcb6 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000029.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000029.xml @@ -82,12 +82,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -146,6 +140,12 @@ def mandatorytest(row, column, index): ${row['pathotype']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000030.xml b/ena_upload/templates/ENA_template_samples_ERC000030.xml index 63f63cd..b11c070 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000030.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000030.xml @@ -141,12 +141,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - broad-scale environmental context @@ -224,6 +218,12 @@ def mandatorytest(row, column, index): mg Chl/m3 + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + Citation diff --git a/ena_upload/templates/ENA_template_samples_ERC000031.xml b/ena_upload/templates/ENA_template_samples_ERC000031.xml index 7a1bc45..fad5c88 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000031.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000031.xml @@ -172,12 +172,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -983,6 +977,12 @@ def mandatorytest(row, column, index): year + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000032.xml b/ena_upload/templates/ENA_template_samples_ERC000032.xml index 3d667a7..9b51ac9 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000032.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000032.xml @@ -177,12 +177,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -216,6 +210,12 @@ def mandatorytest(row, column, index): ${row['sample capture status']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease outcome diff --git a/ena_upload/templates/ENA_template_samples_ERC000033.xml b/ena_upload/templates/ENA_template_samples_ERC000033.xml index 1f2e3c1..ec01815 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000033.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000033.xml @@ -81,12 +81,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -120,6 +114,12 @@ def mandatorytest(row, column, index): ${row['sample capture status']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease outcome diff --git a/ena_upload/templates/ENA_template_samples_ERC000034.xml b/ena_upload/templates/ENA_template_samples_ERC000034.xml index 2ed7797..fab7686 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000034.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000034.xml @@ -45,12 +45,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - sex @@ -75,6 +69,12 @@ def mandatorytest(row, column, index): ${row['diagnosis']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + strain diff --git a/ena_upload/templates/ENA_template_samples_ERC000035.xml b/ena_upload/templates/ENA_template_samples_ERC000035.xml index cab5871..d897cde 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000035.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000035.xml @@ -69,12 +69,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - sampling time point @@ -99,6 +93,12 @@ def mandatorytest(row, column, index): ${row['age']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + phenotype diff --git a/ena_upload/templates/ENA_template_samples_ERC000036.xml b/ena_upload/templates/ENA_template_samples_ERC000036.xml index b0bb3af..c0eb3e6 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000036.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000036.xml @@ -95,12 +95,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -140,6 +134,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + receipt date diff --git a/ena_upload/templates/ENA_template_samples_ERC000037.xml b/ena_upload/templates/ENA_template_samples_ERC000037.xml index a809bbd..dfb641a 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000037.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000037.xml @@ -222,12 +222,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -328,6 +322,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + climate environment diff --git a/ena_upload/templates/ENA_template_samples_ERC000038.xml b/ena_upload/templates/ENA_template_samples_ERC000038.xml index 0768468..b7156cd 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000038.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000038.xml @@ -118,12 +118,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - broad-scale environmental context @@ -199,6 +193,12 @@ def mandatorytest(row, column, index): mg + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + treatment agent diff --git a/ena_upload/templates/ENA_template_samples_ERC000039.xml b/ena_upload/templates/ENA_template_samples_ERC000039.xml index fcba7cf..9629055 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000039.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000039.xml @@ -81,12 +81,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -114,6 +108,12 @@ def mandatorytest(row, column, index): year + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease outcome diff --git a/ena_upload/templates/ENA_template_samples_ERC000040.xml b/ena_upload/templates/ENA_template_samples_ERC000040.xml index 8c3356e..e45722c 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000040.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000040.xml @@ -90,12 +90,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -140,6 +134,12 @@ def mandatorytest(row, column, index): ${row['environmental_sample']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + salinity diff --git a/ena_upload/templates/ENA_template_samples_ERC000041.xml b/ena_upload/templates/ENA_template_samples_ERC000041.xml index f8e3fea..944f751 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000041.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000041.xml @@ -96,12 +96,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (region and locality) @@ -127,6 +121,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + receipt date diff --git a/ena_upload/templates/ENA_template_samples_ERC000043.xml b/ena_upload/templates/ENA_template_samples_ERC000043.xml index e056edf..1d5e8c4 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000043.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000043.xml @@ -64,12 +64,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -104,6 +98,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + light intensity diff --git a/ena_upload/templates/ENA_template_samples_ERC000044.xml b/ena_upload/templates/ENA_template_samples_ERC000044.xml index 5310c50..0c99024 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000044.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000044.xml @@ -69,12 +69,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (region and locality) @@ -88,6 +82,12 @@ def mandatorytest(row, column, index): year + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000045.xml b/ena_upload/templates/ENA_template_samples_ERC000045.xml index 0e8a8df..39a10d2 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000045.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000045.xml @@ -51,18 +51,18 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (region and locality) ${row['geographic location (region and locality)']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + receipt date diff --git a/ena_upload/templates/ENA_template_samples_ERC000047.xml b/ena_upload/templates/ENA_template_samples_ERC000047.xml index 360ffe0..e70f6d8 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000047.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000047.xml @@ -223,12 +223,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -287,6 +281,12 @@ def mandatorytest(row, column, index): ${row['size fraction selected']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + source material identifiers diff --git a/ena_upload/templates/ENA_template_samples_ERC000048.xml b/ena_upload/templates/ENA_template_samples_ERC000048.xml index 94f8141..92745cd 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000048.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000048.xml @@ -198,12 +198,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -262,6 +256,12 @@ def mandatorytest(row, column, index): ${row['size fraction selected']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + source material identifiers diff --git a/ena_upload/templates/ENA_template_samples_ERC000049.xml b/ena_upload/templates/ENA_template_samples_ERC000049.xml index f058963..ff7a7ea 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000049.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000049.xml @@ -246,12 +246,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -310,6 +304,12 @@ def mandatorytest(row, column, index): ${row['size fraction selected']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host scientific name diff --git a/ena_upload/templates/ENA_template_samples_ERC000050.xml b/ena_upload/templates/ENA_template_samples_ERC000050.xml index ddc7d39..2c7de87 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000050.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000050.xml @@ -211,12 +211,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -269,6 +263,12 @@ def mandatorytest(row, column, index): ${row['size fraction selected']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + source material identifiers diff --git a/ena_upload/templates/ENA_template_samples_ERC000051.xml b/ena_upload/templates/ENA_template_samples_ERC000051.xml index c67ad21..41d59b7 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000051.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000051.xml @@ -69,12 +69,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - engrafted tumor sample passage @@ -93,6 +87,12 @@ def mandatorytest(row, column, index): ${row['patient tumor site of collection']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + engraftment host strain name diff --git a/ena_upload/templates/ENA_template_samples_ERC000052.xml b/ena_upload/templates/ENA_template_samples_ERC000052.xml index 20f0111..b102fa9 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000052.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000052.xml @@ -76,12 +76,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -116,6 +110,12 @@ def mandatorytest(row, column, index): years + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/ENA_template_samples_ERC000053.xml b/ena_upload/templates/ENA_template_samples_ERC000053.xml index 963d769..c3129fa 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000053.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000053.xml @@ -145,12 +145,6 @@ def mandatorytest(row, column, index): ${row['collection date']} - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -234,6 +228,12 @@ def mandatorytest(row, column, index): ${row['sex']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + collecting institution diff --git a/ena_upload/templates/ENA_template_samples_ERC000055.xml b/ena_upload/templates/ENA_template_samples_ERC000055.xml index b008d16..17c965e 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000055.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000055.xml @@ -340,12 +340,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -439,6 +433,12 @@ def mandatorytest(row, column, index): ${row['plant structure']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status @@ -899,7 +899,6 @@ def mandatorytest(row, column, index): library preparation kit ${row['library preparation kit']} - % @@ -1036,6 +1035,12 @@ def mandatorytest(row, column, index): ${row['food product type']} + + + plant product + ${row['plant product']} + + relative location of sample diff --git a/ena_upload/templates/ENA_template_samples_ERC000056.xml b/ena_upload/templates/ENA_template_samples_ERC000056.xml index bc6dc8e..4095369 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000056.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000056.xml @@ -475,7 +475,7 @@ def mandatorytest(row, column, index): ${row['assembly name']} - + collection date ${row['collection date']} @@ -488,12 +488,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -667,6 +661,12 @@ def mandatorytest(row, column, index): ${row['sequencing kit']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status @@ -1281,7 +1281,6 @@ def mandatorytest(row, column, index): library preparation kit ${row['library preparation kit']} - % diff --git a/ena_upload/templates/ENA_template_samples_ERC000057.xml b/ena_upload/templates/ENA_template_samples_ERC000057.xml index 6eb68af..4625b61 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000057.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000057.xml @@ -190,7 +190,7 @@ def mandatorytest(row, column, index): ${row['16S recovery software']} - + collection date ${row['collection date']} @@ -203,12 +203,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -273,6 +267,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status @@ -485,6 +485,12 @@ def mandatorytest(row, column, index): ${row['symbiotic host organism life cycle type']} + + + host dependence + ${row['host dependence']} + + host specificity diff --git a/ena_upload/templates/ENA_template_samples_ERC000058.xml b/ena_upload/templates/ENA_template_samples_ERC000058.xml index 5556dae..8ada54e 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000058.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000058.xml @@ -257,7 +257,7 @@ def mandatorytest(row, column, index): ${row['field name']} - + collection date ${row['collection date']} @@ -270,12 +270,6 @@ def mandatorytest(row, column, index): m - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - geographic location (latitude) @@ -367,6 +361,12 @@ def mandatorytest(row, column, index): ${row['sample storage duration']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + host disease status diff --git a/ena_upload/templates/SRA.common.xsd b/ena_upload/templates/SRA.common.xsd index cc04c56..6f68d63 100644 --- a/ena_upload/templates/SRA.common.xsd +++ b/ena_upload/templates/SRA.common.xsd @@ -967,6 +967,7 @@ + @@ -1064,6 +1065,7 @@ +