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robertapeixotorobertapeixoto
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Merge pull request #114 from COMPASS-DOE/handle-no-footer-data
Warn and skip if no smart chamber footer data
2 parents 17dd8fb + a0acb22 commit 0838976

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+136
-2
lines changed

4 files changed

+136
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lines changed

‎DESCRIPTION‎

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@@ -36,6 +36,6 @@ Suggests:
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testthat (>= 3.0.0),
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withr (>= 2.0)
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Config/testthat/edition: 3
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RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3
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VignetteBuilder: knitr
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BugReports: https://github.com/COMPASS-DOE/fluxfinder/issues

‎R/read_data_functions.R‎

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@@ -291,6 +291,15 @@ ffi_read_LIsmartchamber <- function(file, concentrations = TRUE) {
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}
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footer_df <- as.data.frame(footer_info)
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# Sanity check: make sure header and footer have data
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if(nrow(header_df) == 0) {
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warning("No header information for observation ", obs, "; skipping")
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next
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}
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if(nrow(footer_df) == 0) {
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warning("No footer information for observation ", obs, "; skipping")
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next
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}
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# Combine and store; note that the 1-row data frames get
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# replicated to have as many rows as the data
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final_dat[[paste(obs, rep)]] <- cbind(rep_df, header_df, data_df, footer_df)

‎tests/testthat/data/LI8200_bad_no_footer.json‎

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@@ -0,0 +1,121 @@
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{ "name": "LE_CRC_11_7_2022",
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"remark": "",
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"date":1667815847,
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"datasets": [
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{ "TrS33":
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{
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"remark": "",
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"reps":
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{
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"REP_1": {
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"header":{
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"Chamber":"82s-1031",
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"Version":"1.1",
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"InstrumentModel":"generic",
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"InstrumentSerialNumber":"generic",
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"Date":"2022-11-07 12:17:00",
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"RepNum":1,
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"DeadBand":5,
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"Area":318,
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"Offset":5,
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"ChamVolume":4244.1,
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"IrgaVolume":80.46,
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"TotalVolume":5914.56,
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"gps_time":1667841420,
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"latitude":41.622,
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"longitude":-83.2381,
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"gps_hdop":1.05,
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"altitude":178.7,
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"gps_sats":11,
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"TimeZone":"US/Eastern"
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},
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"labels":{
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"area":"Area",
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"volume":"TotalVolume",
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"deadband":"DeadBand",
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"etime":"timestamp",
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"pressure":"chamber_p",
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"temperature":"chamber_t",
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"h2o":""
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},
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"data":{
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"timestamp":[1,2,3,4,5,6,7,8,9,
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10,11,12,13,14,15,16,17,18,19,
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20,21,22,23,24,25,26,27,28,29,
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30,31,32,33,34,35,36,37,38,39,
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40,41,42,43,44,45,46,47,48,49,
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50,51,52,53,54,55,56,57,58,59,
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60],
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"chamber_p":[100.988,100.983,100.989,100.985,100.986,100.979,100.983,100.976,100.981,
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100.982,100.978,100.975,100.971,100.975,100.971,100.972,100.968,100.972,100.977,
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100.973,100.968,100.967,100.968,100.965,101.005,100.996,100.985,100.981,100.979,
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100.975,100.973,100.995,100.995,100.982,100.988,100.987,100.98,100.982,100.979,
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100.983,100.986,100.979,100.979,100.981,100.991,100.981,100.986,100.984,100.983,
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100.987,100.989,100.988,100.984,100.992,100.99,100.987,100.985,100.986,100.988,
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100.989],
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"chamber_p_t":[20.8438,20.8333,20.8646,20.875,20.9062,20.9062,20.9479,20.9375,21.0125,
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21.0417,21.0312,21.0625,21.0729,21.0938,21.1146,21.1458,21.1625,21.1875,21.2292,
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21.2292,21.2292,21.2604,21.2708,21.2917,21.3438,21.3125,21.3438,21.375,21.3958,
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21.4167,21.4062,21.4583,21.4792,21.475,21.5104,21.5417,21.5312,21.5833,21.5833,
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21.625,21.6562,21.6354,21.6625,21.6667,21.7292,21.7083,21.7396,21.75,21.7604,
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21.7917,21.8125,21.8333,21.8333,21.8854,21.8958,21.8854,21.8854,21.9271,21.9375,
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21.975],
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"chamber_t":[16.4906,16.4805,16.4738,16.4724,16.4741,16.4758,16.4785,16.4815,16.4845,
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16.4881,16.4894,16.4884,16.4879,16.4881,16.4876,16.4874,16.4886,16.4908,16.4968,
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16.5034,16.5094,16.5138,16.5197,16.5249,16.5279,16.5307,16.5338,16.5412,16.5484,
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16.5544,16.5573,16.56,16.5647,16.5699,16.5732,16.5776,16.5831,16.5878,16.592,
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16.5999,16.6081,16.6173,16.6273,16.6357,16.6401,16.6446,16.6483,16.6535,16.6617,
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16.6692,16.6735,16.6784,16.6866,16.6941,16.7008,16.7107,16.7177,16.7227,16.7274,
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16.7356],
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"soil_t":[9999,9999,9999,9999,9999,9999,9999,9999,9999,
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9999,9999,9999,9999,9999,9999,9999,9999,9999,9999,
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9999,9999,9999,9999,9999,9999,9999,9999,9999,9999,
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9999,9999,9999,9999,9999,9999,9999,9999,9999,9999,
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9999,9999,9999,9999,9999,9999,9999,9999,9999,9999,
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9999,9999,9999,9999,9999,9999,9999,9999,9999,9999,
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9999],
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"soilp_c":[0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.019,
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0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,
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0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,
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0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,
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0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,
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0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,0.019,
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0.019],
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"soilp_m":[0,0,0,0,0,0,0,0,0.178,
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0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,
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0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,
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0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,
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0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,
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0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,0.178,
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0.178],
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"soilp_t":[16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,
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16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,
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16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,
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16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,
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16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,
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16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,16.7,
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16.7]
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},
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"summary":{
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"timestamp":[0,30.5,59],
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"chamber_p":[100.988,100.982,0.0395813],
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"chamber_p_t":[20.7963,21.415,1.14167],
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"chamber_t":[16.4778,16.5705,0.263294],
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"soil_t":[9999,9999,0],
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"soilp_c":[-0.005,0.0166,0.018],
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"soilp_m":[-0.0593333,0.154267,0.178],
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"soilp_t":[16.7,16.7,0]
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},
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"footer":{
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"P_o":100.988,
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"T_o":16.4778,
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"W_o":0,
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"fluxes":[
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]
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}
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}
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}
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}
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}
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]
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}

‎tests/testthat/test-read_functions.R‎

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@@ -107,9 +107,13 @@ test_that("ffi_read_LIsmartchamber works", {
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expect_true("TIMESTAMP" %in% names(x))
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expect_s3_class(x$TIMESTAMP, "POSIXct")
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# Bad data with no concentration data
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# Bad data -- no concentration data
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expect_warning(ffi_read_LIsmartchamber("data/LI8200-01S-bad-data.json"),
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regexp = "0-row data")
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# Bad data -- no footer
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# (see https://github.com/COMPASS-DOE/fluxfinder/issues/113)
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expect_warning(ffi_read_LIsmartchamber("data/LI8200_bad_no_footer.json"),
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regexp = "No footer")
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})
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test_that("ffi_read_LI850 works", {

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