From 8ae89b376e7cc0f44a76105a846a426810b7e8aa Mon Sep 17 00:00:00 2001 From: bedroesb Date: Mon, 2 May 2022 14:30:55 +0200 Subject: [PATCH] adding units to templates --- .../ENA_template_samples_ERC000012.xml | 22 ++++++ .../ENA_template_samples_ERC000013.xml | 19 +++++ .../ENA_template_samples_ERC000014.xml | 15 ++++ .../ENA_template_samples_ERC000015.xml | 14 ++++ .../ENA_template_samples_ERC000016.xml | 15 ++++ .../ENA_template_samples_ERC000017.xml | 15 ++++ .../ENA_template_samples_ERC000018.xml | 14 ++++ .../ENA_template_samples_ERC000019.xml | 58 +++++++++++++++ .../ENA_template_samples_ERC000020.xml | 17 +++++ .../ENA_template_samples_ERC000021.xml | 53 +++++++++++++ .../ENA_template_samples_ERC000022.xml | 18 +++++ .../ENA_template_samples_ERC000023.xml | 27 +++++++ .../ENA_template_samples_ERC000024.xml | 73 ++++++++++++++++++ .../ENA_template_samples_ERC000025.xml | 40 ++++++++++ .../ENA_template_samples_ERC000027.xml | 74 +++++++++++++++++++ .../ENA_template_samples_ERC000029.xml | 6 ++ .../ENA_template_samples_ERC000030.xml | 10 +++ .../ENA_template_samples_ERC000031.xml | 12 +++ .../ENA_template_samples_ERC000032.xml | 3 + .../ENA_template_samples_ERC000033.xml | 9 +++ .../ENA_template_samples_ERC000034.xml | 1 + .../ENA_template_samples_ERC000036.xml | 7 ++ .../ENA_template_samples_ERC000037.xml | 10 +++ .../ENA_template_samples_ERC000038.xml | 11 +++ .../ENA_template_samples_ERC000039.xml | 3 + .../ENA_template_samples_ERC000040.xml | 5 ++ .../ENA_template_samples_ERC000041.xml | 5 ++ .../ENA_template_samples_ERC000043.xml | 9 +++ .../ENA_template_samples_ERC000047.xml | 9 +++ .../ENA_template_samples_ERC000048.xml | 8 ++ .../ENA_template_samples_ERC000049.xml | 8 ++ .../ENA_template_samples_ERC000050.xml | 9 +++ .../ENA_template_samples_ERC000052.xml | 11 +++ .../ENA_template_samples_ERC000053.xml | 4 + .../jinja_templates/ENA_template_samples.xml | 8 +- var/xml_converter.py | 7 +- 36 files changed, 627 insertions(+), 2 deletions(-) diff --git a/ena_upload/templates/ENA_template_samples_ERC000012.xml b/ena_upload/templates/ENA_template_samples_ERC000012.xml index b035335..e23f238 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000012.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000012.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -197,6 +198,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m geographic location (country and/or sea) @@ -205,10 +207,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -236,12 +240,14 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m ventilation rate ${row['ventilation rate']} + m3/min @@ -284,6 +290,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -302,12 +309,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -332,24 +341,28 @@ def attributetest(row, column): barometric pressure ${row['barometric pressure']} + mm Hg humidity ${row['humidity']} + g/m3 pollutants ${row['pollutants']} + mg/L solar irradiance ${row['solar irradiance']} + W/m2 @@ -362,54 +375,63 @@ def attributetest(row, column): wind speed ${row['wind speed']} + m/s temperature ${row['temperature']} + ºC carbon dioxide ${row['carbon dioxide']} + µmol/L carbon monoxide ${row['carbon monoxide']} + µM/L oxygen ${row['oxygen']} + parts/million respirable particulate matter ${row['respirable particulate matter']} + µg/m3 volatile organic compounds ${row['volatile organic compounds']} + µg/m3 sample salinity ${row['sample salinity']} + psu methane ${row['methane']} + µM/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000013.xml b/ena_upload/templates/ENA_template_samples_ERC000013.xml index 89ab78d..3c64c53 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000013.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000013.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -198,6 +199,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -207,10 +209,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -226,6 +230,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -244,6 +249,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -280,6 +286,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -292,6 +299,7 @@ def attributetest(row, column): host dry mass ${row['host dry mass']} + mg @@ -310,12 +318,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -346,6 +356,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -376,12 +387,14 @@ def attributetest(row, column): host height ${row['host height']} + mm host length ${row['host length']} + mm @@ -400,6 +413,7 @@ def attributetest(row, column): host total mass ${row['host total mass']} + kg @@ -424,6 +438,7 @@ def attributetest(row, column): host body temperature ${row['host body temperature']} + ºC @@ -448,12 +463,14 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC sample salinity ${row['sample salinity']} + psu @@ -466,12 +483,14 @@ def attributetest(row, column): host blood pressure diastolic ${row['host blood pressure diastolic']} + mm Hg host blood pressure systolic ${row['host blood pressure systolic']} + mm Hg diff --git a/ena_upload/templates/ENA_template_samples_ERC000014.xml b/ena_upload/templates/ENA_template_samples_ERC000014.xml index a8a9f47..f50f364 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000014.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000014.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -207,10 +208,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -268,6 +271,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -304,12 +308,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -376,6 +382,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -394,12 +401,14 @@ def attributetest(row, column): host height ${row['host height']} + mm host body-mass index ${row['host body-mass index']} + kg/m2 @@ -418,6 +427,7 @@ def attributetest(row, column): host total mass ${row['host total mass']} + kg @@ -430,6 +440,7 @@ def attributetest(row, column): host body temperature ${row['host body temperature']} + ºC @@ -448,12 +459,14 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC sample salinity ${row['sample salinity']} + psu @@ -478,6 +491,7 @@ def attributetest(row, column): weight loss in last three months ${row['weight loss in last three months']} + kg @@ -538,6 +552,7 @@ def attributetest(row, column): host pulse ${row['host pulse']} + bpm diff --git a/ena_upload/templates/ENA_template_samples_ERC000015.xml b/ena_upload/templates/ENA_template_samples_ERC000015.xml index 527a756..d71bbcd 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000015.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000015.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -201,10 +202,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -262,6 +265,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -292,12 +296,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -340,6 +346,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -352,12 +359,14 @@ def attributetest(row, column): host height ${row['host height']} + mm host body-mass index ${row['host body-mass index']} + kg/m2 @@ -376,6 +385,7 @@ def attributetest(row, column): host total mass ${row['host total mass']} + kg @@ -388,6 +398,7 @@ def attributetest(row, column): host body temperature ${row['host body temperature']} + ºC @@ -400,12 +411,14 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC sample salinity ${row['sample salinity']} + psu @@ -448,6 +461,7 @@ def attributetest(row, column): host pulse ${row['host pulse']} + bpm diff --git a/ena_upload/templates/ENA_template_samples_ERC000016.xml b/ena_upload/templates/ENA_template_samples_ERC000016.xml index 9e3f1e7..54359ae 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000016.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000016.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -201,10 +202,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -262,6 +265,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -292,12 +296,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -334,6 +340,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -346,12 +353,14 @@ def attributetest(row, column): host height ${row['host height']} + mm host body-mass index ${row['host body-mass index']} + kg/m2 @@ -370,6 +379,7 @@ def attributetest(row, column): host total mass ${row['host total mass']} + kg @@ -382,6 +392,7 @@ def attributetest(row, column): host body temperature ${row['host body temperature']} + ºC @@ -394,12 +405,14 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC sample salinity ${row['sample salinity']} + psu @@ -412,6 +425,7 @@ def attributetest(row, column): time since last toothbrushing ${row['time since last toothbrushing']} + minutes @@ -442,6 +456,7 @@ def attributetest(row, column): host pulse ${row['host pulse']} + bpm diff --git a/ena_upload/templates/ENA_template_samples_ERC000017.xml b/ena_upload/templates/ENA_template_samples_ERC000017.xml index 9309833..cf08fb9 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000017.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000017.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -201,10 +202,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -262,6 +265,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -292,12 +296,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -334,6 +340,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -346,12 +353,14 @@ def attributetest(row, column): host height ${row['host height']} + mm host body-mass index ${row['host body-mass index']} + kg/m2 @@ -370,6 +379,7 @@ def attributetest(row, column): host total mass ${row['host total mass']} + kg @@ -382,6 +392,7 @@ def attributetest(row, column): host body temperature ${row['host body temperature']} + ºC @@ -394,12 +405,14 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC sample salinity ${row['sample salinity']} + psu @@ -412,6 +425,7 @@ def attributetest(row, column): time since last wash ${row['time since last wash']} + minutes @@ -448,6 +462,7 @@ def attributetest(row, column): host pulse ${row['host pulse']} + bpm diff --git a/ena_upload/templates/ENA_template_samples_ERC000018.xml b/ena_upload/templates/ENA_template_samples_ERC000018.xml index c30042b..bfc2c5e 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000018.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000018.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -201,10 +202,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -262,6 +265,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -292,12 +296,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -340,6 +346,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -352,12 +359,14 @@ def attributetest(row, column): host height ${row['host height']} + mm host body-mass index ${row['host body-mass index']} + kg/m2 @@ -376,6 +385,7 @@ def attributetest(row, column): host total mass ${row['host total mass']} + kg @@ -388,6 +398,7 @@ def attributetest(row, column): host body temperature ${row['host body temperature']} + ºC @@ -400,12 +411,14 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC sample salinity ${row['sample salinity']} + psu @@ -490,6 +503,7 @@ def attributetest(row, column): host pulse ${row['host pulse']} + bpm diff --git a/ena_upload/templates/ENA_template_samples_ERC000019.xml b/ena_upload/templates/ENA_template_samples_ERC000019.xml index 8af01c6..1286b4c 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000019.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000019.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -198,6 +199,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -207,10 +209,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -225,6 +229,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m environment (biome) @@ -241,6 +246,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -276,12 +282,14 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 biomass ${row['biomass']} + t @@ -300,12 +308,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -330,36 +340,42 @@ def attributetest(row, column): alkalinity ${row['alkalinity']} + mEq/L mean friction velocity ${row['mean friction velocity']} + m/s mean peak friction velocity ${row['mean peak friction velocity']} + m/s pressure ${row['pressure']} + bar temperature ${row['temperature']} + ºC turbidity ${row['turbidity']} + NTU @@ -372,42 +388,49 @@ def attributetest(row, column): alkyl diethers ${row['alkyl diethers']} + µg/L aminopeptidase activity ${row['aminopeptidase activity']} + mol/L/h ammonium ${row['ammonium']} + µmol/L bacterial carbon production ${row['bacterial carbon production']} + ng/h bishomohopanol ${row['bishomohopanol']} + µg/g bromide ${row['bromide']} + µmol/L calcium ${row['calcium']} + µmol/L @@ -420,210 +443,245 @@ def attributetest(row, column): chloride ${row['chloride']} + mg/L chlorophyll ${row['chlorophyll']} + µg/L diether lipids ${row['diether lipids']} + ng/L dissolved carbon dioxide ${row['dissolved carbon dioxide']} + µmol/L dissolved hydrogen ${row['dissolved hydrogen']} + µmol/L dissolved inorganic carbon ${row['dissolved inorganic carbon']} + µg/L dissolved organic carbon ${row['dissolved organic carbon']} + µmol/L dissolved organic nitrogen ${row['dissolved organic nitrogen']} + µg/L methane ${row['methane']} + µM/L dissolved oxygen ${row['dissolved oxygen']} + µmol/kg glucosidase activity ${row['glucosidase activity']} + mol/L/h magnesium ${row['magnesium']} + parts/million n-alkanes ${row['n-alkanes']} + µmol/L nitrate ${row['nitrate']} + µmol/L nitrite ${row['nitrite']} + µmol/L nitrogen ${row['nitrogen']} + µmol/L organic carbon ${row['organic carbon']} + µmol/L organic matter ${row['organic matter']} + µg/L organic nitrogen ${row['organic nitrogen']} + µg/L particulate organic carbon ${row['particulate organic carbon']} + µg/L petroleum hydrocarbon ${row['petroleum hydrocarbon']} + µmol/L phaeopigments ${row['phaeopigments']} + µg/L phosphate ${row['phosphate']} + µmol/L phospholipid fatty acid ${row['phospholipid fatty acid']} + mol/g potassium ${row['potassium']} + µmol/L redox potential ${row['redox potential']} + mV salinity ${row['salinity']} + psu total carbon ${row['total carbon']} + µg/L silicate ${row['silicate']} + µmol/L sodium ${row['sodium']} + µmol/L total organic carbon ${row['total organic carbon']} + g/kg water content ${row['water content']} + g/g sulfate ${row['sulfate']} + µmol/L sulfide ${row['sulfide']} + µmol/L total nitrogen ${row['total nitrogen']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000020.xml b/ena_upload/templates/ENA_template_samples_ERC000020.xml index d26699d..0de3257 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000020.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000020.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -198,6 +199,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -207,10 +209,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -226,6 +230,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -244,6 +249,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -280,12 +286,14 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 host dry mass ${row['host dry mass']} + mg @@ -310,18 +318,21 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C host wet mass ${row['host wet mass']} + mg @@ -346,6 +357,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -364,12 +376,14 @@ def attributetest(row, column): host height ${row['host height']} + mm host length ${row['host length']} + mm @@ -382,6 +396,7 @@ def attributetest(row, column): host total mass ${row['host total mass']} + kg @@ -424,12 +439,14 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC sample salinity ${row['sample salinity']} + psu diff --git a/ena_upload/templates/ENA_template_samples_ERC000021.xml b/ena_upload/templates/ENA_template_samples_ERC000021.xml index 50ecca6..fc3d24e 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000021.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000021.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -198,6 +199,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -207,10 +209,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -225,6 +229,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m environment (biome) @@ -241,6 +246,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -276,18 +282,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 biomass ${row['biomass']} + t density ${row['density']} + g/m3 @@ -306,12 +315,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -336,42 +347,49 @@ def attributetest(row, column): alkyl diethers ${row['alkyl diethers']} + µg/L aminopeptidase activity ${row['aminopeptidase activity']} + mol/L/h ammonium ${row['ammonium']} + µmol/L bacterial carbon production ${row['bacterial carbon production']} + ng/h bishomohopanol ${row['bishomohopanol']} + µg/g bromide ${row['bromide']} + µmol/L calcium ${row['calcium']} + µmol/L @@ -384,210 +402,245 @@ def attributetest(row, column): chloride ${row['chloride']} + mg/L chlorophyll ${row['chlorophyll']} + µg/L diether lipids ${row['diether lipids']} + ng/L dissolved carbon dioxide ${row['dissolved carbon dioxide']} + µmol/L dissolved hydrogen ${row['dissolved hydrogen']} + µmol/L dissolved inorganic carbon ${row['dissolved inorganic carbon']} + µg/L dissolved organic carbon ${row['dissolved organic carbon']} + µmol/L dissolved organic nitrogen ${row['dissolved organic nitrogen']} + µg/L methane ${row['methane']} + µM/L dissolved oxygen ${row['dissolved oxygen']} + µmol/kg glucosidase activity ${row['glucosidase activity']} + mol/L/h magnesium ${row['magnesium']} + parts/million n-alkanes ${row['n-alkanes']} + µmol/L nitrate ${row['nitrate']} + µmol/L nitrite ${row['nitrite']} + µmol/L nitrogen ${row['nitrogen']} + µmol/L organic carbon ${row['organic carbon']} + µmol/L organic matter ${row['organic matter']} + µg/L organic nitrogen ${row['organic nitrogen']} + µg/L particulate organic carbon ${row['particulate organic carbon']} + µg/L petroleum hydrocarbon ${row['petroleum hydrocarbon']} + µmol/L phaeopigments ${row['phaeopigments']} + µg/L phosphate ${row['phosphate']} + µmol/L phospholipid fatty acid ${row['phospholipid fatty acid']} + mol/g potassium ${row['potassium']} + µmol/L redox potential ${row['redox potential']} + mV salinity ${row['salinity']} + psu total carbon ${row['total carbon']} + µg/L silicate ${row['silicate']} + µmol/L sodium ${row['sodium']} + µmol/L total organic carbon ${row['total organic carbon']} + g/kg water content ${row['water content']} + g/g sulfate ${row['sulfate']} + µmol/L sulfide ${row['sulfide']} + µmol/L total nitrogen ${row['total nitrogen']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000022.xml b/ena_upload/templates/ENA_template_samples_ERC000022.xml index b129c40..632f1ec 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000022.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000022.xml @@ -26,6 +26,7 @@ def attributetest(row, column): slope gradient ${row['slope gradient']} + % @@ -96,6 +97,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -222,6 +224,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -231,10 +234,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -249,6 +254,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m environment (biome) @@ -265,6 +271,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -300,6 +307,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -312,6 +320,7 @@ def attributetest(row, column): sample weight for DNA extraction ${row['sample weight for DNA extraction']} + g @@ -324,6 +333,7 @@ def attributetest(row, column): microbial biomass ${row['microbial biomass']} + g/kg @@ -336,6 +346,7 @@ def attributetest(row, column): extreme_unusual_properties/salinity ${row['extreme_unusual_properties/salinity']} + psu @@ -360,6 +371,7 @@ def attributetest(row, column): extreme_unusual_properties/Al saturation ${row['extreme_unusual_properties/Al saturation']} + % @@ -432,12 +444,14 @@ def attributetest(row, column): mean annual and seasonal temperature ${row['mean annual and seasonal temperature']} + ºC mean annual and seasonal precipitation ${row['mean annual and seasonal precipitation']} + mm @@ -480,6 +494,7 @@ def attributetest(row, column): texture ${row['texture']} + % sand/silt/clay @@ -522,18 +537,21 @@ def attributetest(row, column): total organic carbon ${row['total organic carbon']} + g/kg water content ${row['water content']} + g/g total nitrogen ${row['total nitrogen']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000023.xml b/ena_upload/templates/ENA_template_samples_ERC000023.xml index 0e16a66..a2270b1 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000023.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000023.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -201,10 +202,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -220,6 +223,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -268,6 +272,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -286,12 +291,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -304,12 +311,14 @@ def attributetest(row, column): biochemical oxygen demand ${row['biochemical oxygen demand']} + mg/L (over 5 days at 20C) chemical oxygen demand ${row['chemical oxygen demand']} + mg/L (over 5 days at 20C) @@ -340,6 +349,7 @@ def attributetest(row, column): sludge retention time ${row['sludge retention time']} + weeks @@ -364,12 +374,14 @@ def attributetest(row, column): alkalinity ${row['alkalinity']} + mEq/L industrial effluent percent ${row['industrial effluent percent']} + % @@ -388,6 +400,7 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC @@ -400,84 +413,98 @@ def attributetest(row, column): efficiency percent ${row['efficiency percent']} + % emulsions ${row['emulsions']} + µg/L gaseous substances ${row['gaseous substances']} + µmol/L inorganic particles ${row['inorganic particles']} + mol/L organic particles ${row['organic particles']} + g/L sample salinity ${row['sample salinity']} + psu soluble inorganic material ${row['soluble inorganic material']} + parts/million soluble organic material ${row['soluble organic material']} + parts/million suspended solids ${row['suspended solids']} + parts/million total phosphate ${row['total phosphate']} + µmol/L nitrate ${row['nitrate']} + µmol/L phosphate ${row['phosphate']} + µmol/L sodium ${row['sodium']} + µmol/L total nitrogen ${row['total nitrogen']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000024.xml b/ena_upload/templates/ENA_template_samples_ERC000024.xml index 43c5750..52a5d60 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000024.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000024.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -198,6 +199,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -207,10 +209,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -225,6 +229,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m environment (biome) @@ -242,6 +247,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -278,18 +284,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 biomass ${row['biomass']} + t density ${row['density']} + g/m3 @@ -308,12 +317,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -338,6 +349,7 @@ def attributetest(row, column): alkalinity ${row['alkalinity']} + mEq/L @@ -350,60 +362,70 @@ def attributetest(row, column): conductivity ${row['conductivity']} + mS/cm water current ${row['water current']} + m3/s fluorescence ${row['fluorescence']} + mg Chla/m3 light intensity ${row['light intensity']} + lux mean friction velocity ${row['mean friction velocity']} + m/s mean peak friction velocity ${row['mean peak friction velocity']} + m/s downward PAR ${row['downward PAR']} + µE/m2/s photon flux ${row['photon flux']} + µmol/m2/s pressure ${row['pressure']} + bar temperature ${row['temperature']} + ºC @@ -422,60 +444,70 @@ def attributetest(row, column): total depth of water column ${row['total depth of water column']} + m alkyl diethers ${row['alkyl diethers']} + µg/L aminopeptidase activity ${row['aminopeptidase activity']} + mol/L/h ammonium ${row['ammonium']} + µmol/L bacterial carbon production ${row['bacterial carbon production']} + ng/h bacterial production ${row['bacterial production']} + mg/m3/d bacterial respiration ${row['bacterial respiration']} + mg/m3/d bishomohopanol ${row['bishomohopanol']} + µg/g bromide ${row['bromide']} + µmol/L calcium ${row['calcium']} + µmol/L @@ -488,246 +520,287 @@ def attributetest(row, column): chloride ${row['chloride']} + mg/L chlorophyll ${row['chlorophyll']} + µg/L diether lipids ${row['diether lipids']} + ng/L dissolved carbon dioxide ${row['dissolved carbon dioxide']} + µmol/L dissolved hydrogen ${row['dissolved hydrogen']} + µmol/L dissolved inorganic carbon ${row['dissolved inorganic carbon']} + µg/L dissolved inorganic nitrogen ${row['dissolved inorganic nitrogen']} + µg/L dissolved inorganic phosphorus ${row['dissolved inorganic phosphorus']} + µg/L dissolved organic carbon ${row['dissolved organic carbon']} + µmol/L dissolved organic nitrogen ${row['dissolved organic nitrogen']} + µg/L dissolved oxygen ${row['dissolved oxygen']} + µmol/kg glucosidase activity ${row['glucosidase activity']} + mol/L/h magnesium ${row['magnesium']} + parts/million n-alkanes ${row['n-alkanes']} + µmol/L nitrate ${row['nitrate']} + µmol/L nitrite ${row['nitrite']} + µmol/L nitrogen ${row['nitrogen']} + µmol/L organic carbon ${row['organic carbon']} + µmol/L organic matter ${row['organic matter']} + µg/L organic nitrogen ${row['organic nitrogen']} + µg/L particulate organic carbon ${row['particulate organic carbon']} + µg/L particulate organic nitrogen ${row['particulate organic nitrogen']} + µg/L petroleum hydrocarbon ${row['petroleum hydrocarbon']} + µmol/L phaeopigments ${row['phaeopigments']} + µg/L phosphate ${row['phosphate']} + µmol/L phospholipid fatty acid ${row['phospholipid fatty acid']} + mol/g potassium ${row['potassium']} + µmol/L primary production ${row['primary production']} + mg/m3/day redox potential ${row['redox potential']} + mV salinity ${row['salinity']} + psu silicate ${row['silicate']} + µmol/L sodium ${row['sodium']} + µmol/L soluble reactive phosphorus ${row['soluble reactive phosphorus']} + µmol/L sulfate ${row['sulfate']} + µmol/L sulfide ${row['sulfide']} + µmol/L suspended particulate matter ${row['suspended particulate matter']} + mg/L total dissolved nitrogen ${row['total dissolved nitrogen']} + µg/L total inorganic nitrogen ${row['total inorganic nitrogen']} + µg/L total nitrogen ${row['total nitrogen']} + µmol/L total particulate carbon ${row['total particulate carbon']} + µmol/L total phosphorus ${row['total phosphorus']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000025.xml b/ena_upload/templates/ENA_template_samples_ERC000025.xml index d2a78d8..438646f 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000025.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000025.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -198,6 +199,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -207,10 +209,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -226,6 +230,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -244,6 +249,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -280,18 +286,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 biomass ${row['biomass']} + t density ${row['density']} + g/m3 @@ -310,12 +319,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -340,24 +351,28 @@ def attributetest(row, column): alkalinity ${row['alkalinity']} + mEq/L water current ${row['water current']} + m3/s pressure ${row['pressure']} + bar temperature ${row['temperature']} + ºC @@ -370,150 +385,175 @@ def attributetest(row, column): ammonium ${row['ammonium']} + µmol/L bromide ${row['bromide']} + µmol/L calcium ${row['calcium']} + µmol/L chloride ${row['chloride']} + mg/L chlorophyll ${row['chlorophyll']} + µg/L diether lipids ${row['diether lipids']} + ng/L dissolved carbon dioxide ${row['dissolved carbon dioxide']} + µmol/L dissolved hydrogen ${row['dissolved hydrogen']} + µmol/L dissolved inorganic carbon ${row['dissolved inorganic carbon']} + µg/L dissolved organic nitrogen ${row['dissolved organic nitrogen']} + µg/L dissolved oxygen ${row['dissolved oxygen']} + µmol/kg nitrate ${row['nitrate']} + µmol/L nitrite ${row['nitrite']} + µmol/L nitrogen ${row['nitrogen']} + µmol/L organic carbon ${row['organic carbon']} + µmol/L organic matter ${row['organic matter']} + µg/L organic nitrogen ${row['organic nitrogen']} + µg/L phosphate ${row['phosphate']} + µmol/L phospholipid fatty acid ${row['phospholipid fatty acid']} + mol/g potassium ${row['potassium']} + µmol/L salinity ${row['salinity']} + psu silicate ${row['silicate']} + µmol/L sodium ${row['sodium']} + µmol/L sulfate ${row['sulfate']} + µmol/L sulfide ${row['sulfide']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000027.xml b/ena_upload/templates/ENA_template_samples_ERC000027.xml index c24d787..d14b20b 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000027.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000027.xml @@ -29,26 +29,31 @@ def attributetest(row, column): Latitude Start ${row['Latitude Start']} + DD Longitude Start ${row['Longitude Start']} + DD Latitude End ${row['Latitude End']} + DD Longitude End ${row['Longitude End']} + DD Depth ${row['Depth']} + m Protocol Label @@ -110,6 +115,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -276,18 +282,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 biomass ${row['biomass']} + t density ${row['density']} + g/m3 @@ -306,12 +315,14 @@ def attributetest(row, column): sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -327,10 +338,12 @@ def attributetest(row, column): Temperature ${row['Temperature']} + ºC Salinity ${row['Salinity']} + psu @@ -348,6 +361,7 @@ def attributetest(row, column): alkalinity ${row['alkalinity']} + mEq/L @@ -360,54 +374,63 @@ def attributetest(row, column): conductivity ${row['conductivity']} + mS/cm water current ${row['water current']} + m3/s fluorescence ${row['fluorescence']} + mg Chla/m3 light intensity ${row['light intensity']} + lux mean friction velocity ${row['mean friction velocity']} + m/s mean peak friction velocity ${row['mean peak friction velocity']} + m/s downward PAR ${row['downward PAR']} + µE/m2/s photon flux ${row['photon flux']} + µmol/m2/s pressure ${row['pressure']} + bar @@ -420,6 +443,7 @@ def attributetest(row, column): turbidity ${row['turbidity']} + NTU @@ -432,60 +456,70 @@ def attributetest(row, column): total depth of water column ${row['total depth of water column']} + m alkyl diethers ${row['alkyl diethers']} + µg/L aminopeptidase activity ${row['aminopeptidase activity']} + mol/L/h ammonium ${row['ammonium']} + µmol/L bacterial carbon production ${row['bacterial carbon production']} + ng/h bacterial production ${row['bacterial production']} + mg/m3/d bacterial respiration ${row['bacterial respiration']} + mg/m3/d bishomohopanol ${row['bishomohopanol']} + µg/g bromide ${row['bromide']} + µmol/L calcium ${row['calcium']} + µmol/L @@ -498,240 +532,280 @@ def attributetest(row, column): chloride ${row['chloride']} + mg/L chlorophyll ${row['chlorophyll']} + µg/L diether lipids ${row['diether lipids']} + ng/L dissolved carbon dioxide ${row['dissolved carbon dioxide']} + µmol/L dissolved hydrogen ${row['dissolved hydrogen']} + µmol/L dissolved inorganic carbon ${row['dissolved inorganic carbon']} + µg/L dissolved inorganic nitrogen ${row['dissolved inorganic nitrogen']} + µg/L dissolved inorganic phosphorus ${row['dissolved inorganic phosphorus']} + µg/L dissolved organic carbon ${row['dissolved organic carbon']} + µmol/L dissolved organic nitrogen ${row['dissolved organic nitrogen']} + µg/L dissolved oxygen ${row['dissolved oxygen']} + µmol/kg glucosidase activity ${row['glucosidase activity']} + mol/L/h magnesium ${row['magnesium']} + parts/million n-alkanes ${row['n-alkanes']} + µmol/L nitrate ${row['nitrate']} + µmol/L nitrite ${row['nitrite']} + µmol/L nitrogen ${row['nitrogen']} + µmol/L organic carbon ${row['organic carbon']} + µmol/L organic matter ${row['organic matter']} + µg/L organic nitrogen ${row['organic nitrogen']} + µg/L particulate organic carbon ${row['particulate organic carbon']} + µg/L particulate organic nitrogen ${row['particulate organic nitrogen']} + µg/L petroleum hydrocarbon ${row['petroleum hydrocarbon']} + µmol/L phaeopigments ${row['phaeopigments']} + µg/L phosphate ${row['phosphate']} + µmol/L phospholipid fatty acid ${row['phospholipid fatty acid']} + mol/g potassium ${row['potassium']} + µmol/L primary production ${row['primary production']} + mg/m3/day redox potential ${row['redox potential']} + mV silicate ${row['silicate']} + µmol/L sodium ${row['sodium']} + µmol/L soluble reactive phosphorus ${row['soluble reactive phosphorus']} + µmol/L sulfate ${row['sulfate']} + µmol/L sulfide ${row['sulfide']} + µmol/L suspended particulate matter ${row['suspended particulate matter']} + mg/L total dissolved nitrogen ${row['total dissolved nitrogen']} + µg/L total inorganic nitrogen ${row['total inorganic nitrogen']} + µg/L total nitrogen ${row['total nitrogen']} + µmol/L total particulate carbon ${row['total particulate carbon']} + µmol/L total phosphorus ${row['total phosphorus']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000029.xml b/ena_upload/templates/ENA_template_samples_ERC000029.xml index df249a6..c315654 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000029.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000029.xml @@ -64,6 +64,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -73,10 +74,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -94,12 +97,14 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -146,6 +151,7 @@ def attributetest(row, column): host age ${row['host age']} + years diff --git a/ena_upload/templates/ENA_template_samples_ERC000030.xml b/ena_upload/templates/ENA_template_samples_ERC000030.xml index 1c5bfad..225b3b0 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000030.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000030.xml @@ -41,26 +41,31 @@ def attributetest(row, column): Latitude Start ${row['Latitude Start']} + DD Longitude Start ${row['Longitude Start']} + DD Latitude End ${row['Latitude End']} + DD Longitude End ${row['Longitude End']} + DD Depth ${row['Depth']} + m @@ -135,27 +140,32 @@ def attributetest(row, column): Salinity Sensor ${row['Salinity Sensor']} + psu Oxygen Sensor ${row['Oxygen Sensor']} + µmol/kg Nitrate Sensor ${row['Nitrate Sensor']} + µmol/L Temperature ${row['Temperature']} + ºC Chlorophyll Sensor ${row['Chlorophyll Sensor']} + mg Chl/m3 diff --git a/ena_upload/templates/ENA_template_samples_ERC000031.xml b/ena_upload/templates/ENA_template_samples_ERC000031.xml index da0df22..dc8bc45 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000031.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000031.xml @@ -78,6 +78,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -201,10 +202,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -330,6 +333,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 @@ -357,31 +361,37 @@ def attributetest(row, column): relative air humidity ${row['relative air humidity']} + % absolute air humidity ${row['absolute air humidity']} + kg surface humidity ${row['surface humidity']} + % air temperature ${row['air temperature']} + ºC surface temperature ${row['surface temperature']} + ºC surface moisture ${row['surface moisture']} + parts/million @@ -394,11 +404,13 @@ def attributetest(row, column): dew point ${row['dew point']} + ºC carbon dioxide ${row['carbon dioxide']} + µmol/L diff --git a/ena_upload/templates/ENA_template_samples_ERC000032.xml b/ena_upload/templates/ENA_template_samples_ERC000032.xml index 3b9d32a..eeee28a 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000032.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000032.xml @@ -174,12 +174,14 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -212,6 +214,7 @@ def attributetest(row, column): host age ${row['host age']} + years diff --git a/ena_upload/templates/ENA_template_samples_ERC000033.xml b/ena_upload/templates/ENA_template_samples_ERC000033.xml index 46e57d8..1e556fa 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000033.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000033.xml @@ -78,12 +78,14 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -116,6 +118,7 @@ def attributetest(row, column): host age ${row['host age']} + years @@ -126,6 +129,12 @@ def attributetest(row, column): host sex ${row['host sex']} + + + lab_host + ${row['lab_host']} + + host scientific name ${row['host scientific name']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000034.xml b/ena_upload/templates/ENA_template_samples_ERC000034.xml index 311846f..e390b9f 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000034.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000034.xml @@ -66,6 +66,7 @@ def attributetest(row, column): treatment dose ${row['treatment dose']} + picomolar diff --git a/ena_upload/templates/ENA_template_samples_ERC000036.xml b/ena_upload/templates/ENA_template_samples_ERC000036.xml index 672de58..ffa958a 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000036.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000036.xml @@ -62,12 +62,14 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -80,18 +82,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -110,6 +115,7 @@ def attributetest(row, column): sample transportation temperature ${row['sample transportation temperature']} + °C @@ -138,6 +144,7 @@ def attributetest(row, column): temperature ${row['temperature']} + ºC diff --git a/ena_upload/templates/ENA_template_samples_ERC000037.xml b/ena_upload/templates/ENA_template_samples_ERC000037.xml index 12e0548..92ce7af 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000037.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000037.xml @@ -50,6 +50,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -66,6 +67,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -75,10 +77,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -96,6 +100,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -114,6 +119,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -148,18 +154,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -378,6 +387,7 @@ def attributetest(row, column): texture ${row['texture']} + % sand/silt/clay diff --git a/ena_upload/templates/ENA_template_samples_ERC000038.xml b/ena_upload/templates/ENA_template_samples_ERC000038.xml index 4852515..999ae65 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000038.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000038.xml @@ -29,14 +29,17 @@ def attributetest(row, column): Latitude Start ${row['Latitude Start']} + DD Longitude Start ${row['Longitude Start']} + DD Depth ${row['Depth']} + m @@ -111,41 +114,49 @@ def attributetest(row, column): shellfish total weight ${row['shellfish total weight']} + g shellfish soft tissue weight ${row['shellfish soft tissue weight']} + g shell length ${row['shell length']} + g shell width ${row['shell width']} + g adductor weight ${row['adductor weight']} + g gonad weight ${row['gonad weight']} + g shell markings ${row['shell markings']} + g toxin burden ${row['toxin burden']} + mg diff --git a/ena_upload/templates/ENA_template_samples_ERC000039.xml b/ena_upload/templates/ENA_template_samples_ERC000039.xml index 93c057e..050f987 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000039.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000039.xml @@ -70,12 +70,14 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -112,6 +114,7 @@ def attributetest(row, column): host age ${row['host age']} + years diff --git a/ena_upload/templates/ENA_template_samples_ERC000040.xml b/ena_upload/templates/ENA_template_samples_ERC000040.xml index 42f63ef..df4f44a 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000040.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000040.xml @@ -66,6 +66,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -75,10 +76,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -90,6 +93,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -118,6 +122,7 @@ def attributetest(row, column): Salinity ${row['Salinity']} + psu diff --git a/ena_upload/templates/ENA_template_samples_ERC000041.xml b/ena_upload/templates/ENA_template_samples_ERC000041.xml index b77db32..d4debb3 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000041.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000041.xml @@ -56,6 +56,7 @@ def attributetest(row, column): DNA concentration ${row['DNA concentration']} + ng/µl @@ -86,18 +87,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -116,6 +120,7 @@ def attributetest(row, column): sample transportation temperature ${row['sample transportation temperature']} + °C diff --git a/ena_upload/templates/ENA_template_samples_ERC000043.xml b/ena_upload/templates/ENA_template_samples_ERC000043.xml index 003e3c3..fa53bd3 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000043.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000043.xml @@ -26,6 +26,7 @@ def attributetest(row, column): Depth ${row['Depth']} + m @@ -50,12 +51,14 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -74,18 +77,21 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 sample storage duration ${row['sample storage duration']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -98,12 +104,14 @@ def attributetest(row, column): Temperature ${row['Temperature']} + ºC Salinity ${row['Salinity']} + psu @@ -116,6 +124,7 @@ def attributetest(row, column): light intensity ${row['light intensity']} + lux diff --git a/ena_upload/templates/ENA_template_samples_ERC000047.xml b/ena_upload/templates/ENA_template_samples_ERC000047.xml index a974f1d..694f674 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000047.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000047.xml @@ -157,6 +157,7 @@ def attributetest(row, column): completeness score ${row['completeness score']} + % completeness software @@ -171,6 +172,7 @@ def attributetest(row, column): contamination score ${row['contamination score']} + % @@ -198,6 +200,7 @@ def attributetest(row, column): reassembly post binning ${row['reassembly post binning']} + Yes @@ -240,6 +243,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -249,10 +253,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -264,6 +270,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -282,6 +289,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -306,6 +314,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 diff --git a/ena_upload/templates/ENA_template_samples_ERC000048.xml b/ena_upload/templates/ENA_template_samples_ERC000048.xml index 1e425ab..cbc8928 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000048.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000048.xml @@ -157,6 +157,7 @@ def attributetest(row, column): completeness score ${row['completeness score']} + % completeness software @@ -171,6 +172,7 @@ def attributetest(row, column): contamination score ${row['contamination score']} + % @@ -244,6 +246,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -253,10 +256,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -268,6 +273,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -286,6 +292,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -310,6 +317,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 diff --git a/ena_upload/templates/ENA_template_samples_ERC000049.xml b/ena_upload/templates/ENA_template_samples_ERC000049.xml index a63ff04..1ee4001 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000049.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000049.xml @@ -152,6 +152,7 @@ def attributetest(row, column): completeness score ${row['completeness score']} + % @@ -176,6 +177,7 @@ def attributetest(row, column): reassembly post binning ${row['reassembly post binning']} + Yes @@ -306,6 +308,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -315,10 +318,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -330,6 +335,7 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m @@ -348,6 +354,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -372,6 +379,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 diff --git a/ena_upload/templates/ENA_template_samples_ERC000050.xml b/ena_upload/templates/ENA_template_samples_ERC000050.xml index 6bf6a1d..3c10c19 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000050.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000050.xml @@ -134,6 +134,7 @@ def attributetest(row, column): completeness score ${row['completeness score']} + % @@ -152,6 +153,7 @@ def attributetest(row, column): contamination score ${row['contamination score']} + % @@ -180,6 +182,7 @@ def attributetest(row, column): reassembly post binning ${row['reassembly post binning']} + Yes @@ -226,6 +229,7 @@ def attributetest(row, column): geographic location (altitude) ${row['geographic location (altitude)']} + m @@ -235,15 +239,18 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD geographic location (depth) ${row['geographic location (depth)']} + m @@ -262,6 +269,7 @@ def attributetest(row, column): geographic location (elevation) ${row['geographic location (elevation)']} + m @@ -286,6 +294,7 @@ def attributetest(row, column): amount or size of sample collected ${row['amount or size of sample collected']} + m3 diff --git a/ena_upload/templates/ENA_template_samples_ERC000052.xml b/ena_upload/templates/ENA_template_samples_ERC000052.xml index 366e9c5..91a676c 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000052.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000052.xml @@ -29,6 +29,7 @@ def attributetest(row, column): sample volume or weight for DNA extraction ${row['sample volume or weight for DNA extraction']} + ng @@ -72,12 +73,14 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD @@ -90,16 +93,19 @@ def attributetest(row, column): trial length ${row['trial length']} + years trial timepoint ${row['trial timepoint']} + years sample storage temperature ${row['sample storage temperature']} + °C @@ -146,12 +152,14 @@ def attributetest(row, column): host length ${row['host length']} + mm host total mass ${row['host total mass']} + kg @@ -176,6 +184,7 @@ def attributetest(row, column): host gutted mass ${row['host gutted mass']} + kg @@ -192,6 +201,7 @@ def attributetest(row, column): host diet treatment concentration ${row['host diet treatment concentration']} + % mass @@ -210,6 +220,7 @@ def attributetest(row, column): host storage container temperature ${row['host storage container temperature']} + °C diff --git a/ena_upload/templates/ENA_template_samples_ERC000053.xml b/ena_upload/templates/ENA_template_samples_ERC000053.xml index 34ef511..4ba9efa 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000053.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000053.xml @@ -61,10 +61,12 @@ def attributetest(row, column): geographic location (latitude) ${row['geographic location (latitude)']} + DD geographic location (longitude) ${row['geographic location (longitude)']} + DD geographic location (region and locality) @@ -80,12 +82,14 @@ def attributetest(row, column): geographic location (depth) ${row['geographic location (depth)']} + m geographic location (elevation) ${row['geographic location (elevation)']} + m diff --git a/ena_upload/templates/jinja_templates/ENA_template_samples.xml b/ena_upload/templates/jinja_templates/ENA_template_samples.xml index 8a27afa..ee30272 100755 --- a/ena_upload/templates/jinja_templates/ENA_template_samples.xml +++ b/ena_upload/templates/jinja_templates/ENA_template_samples.xml @@ -23,16 +23,22 @@ def attributetest(row, column): ${row.sample_description} {%- for key, value in attributes.items() %} - {%- if value == 'mandatory' %} + {%- if value['cardinality'].lower() == 'mandatory' %} {{key}} ${row['{{key}}']} + {%- if value['units'] %} + {{value['units']}} + {%- endif %} {%- else %} {{key}} ${row['{{key}}']} + {%- if value['units'] %} + {{value['units']}} + {%- endif %} {%- endif %} diff --git a/var/xml_converter.py b/var/xml_converter.py index 928548b..500ead2 100644 --- a/var/xml_converter.py +++ b/var/xml_converter.py @@ -55,12 +55,17 @@ def main(): for attribute in root.iter('FIELD'): name = '' cardinality = '' + units = '' for sub_attr in attribute: if sub_attr.tag == 'NAME': name = sub_attr.text elif sub_attr.tag == 'MANDATORY': cardinality = sub_attr.text - xml_tree[name] = cardinality + elif sub_attr.tag == 'UNITS': + for unit in sub_attr: + units = unit.text + cardinality = sub_attr.text + xml_tree[name] = {'cardinality': cardinality, 'units': units} # Loading the xml jinja2 template for samples t = env.get_template('ENA_template_samples.xml')