This document outlines an updated format for events that follows the format used in the fieldactivity nested within a geoJSON data structure.
The format is a GeoJSON FeatureCollection. Each Feature in the collection represents a single site. The properties of each feature contain an array of events that occurred at that site.
The properties are aligned with the fieldactivity schema defined in ui_structure.json.
| # | Category / File | Symptom / Error (abridged) | Root Cause / Context | Fix applied (see commit/patch) |
|---|---|---|---|---|
| 1 | GitHub Pages deploy.github/workflows/publish.yaml |
deploy-pages 404 – “Getting signed artifact URL failed” |
Deploy job could not find a Pages‑type artifact | Switched to actions/upload-artifact@v4 and named it github-pages, which deploy-pages@v4 accepts |
| 2 | Actions tag mismatch | “Missing download info for actions/upload‑artifact@v3” | Referenced tag never existed | Bumped to `upl |
| library(tidyverse) | |
| # system.time(load("~/ccmmf/LandIQ_data/crops_all_years.RData")) | |
| crops_all <- data.table::fread( # ~50% faster than load! | |
| "~/ccmmf/LandIQ_data/crops_all_years.csv" | |
| ) | |
| dwr_2018 <- terra::vect( | |
| "~/ccmmf/LandIQ_data/LandIQ_shapefiles/i15_Crop_Mapping_2018_SHP/i15_Crop_Mapping_2018.shp" | |
| ) |> | |
| terra::project("epsg:3310") | |
| library(xml2) | |
| library(yaml) | |
| # note: does not handle XML attributes or namespaces. | |
| # should work for simple xml structure used by PEcAn | |
| # Convert XML to YAML | |
| xml2yml <- function(xml_string) { | |
| yaml_string <- xml_string |> | |
| read_xml() |> |
| # to get the original version of the eCO2 file | |
| download.file('https://github.com/cran/SoilR/raw/1.1-23/data/eCO2.rda', | |
| 'eCO2.rda') | |
| load('eCO2.rda') | |
| library(SoilR) | |
| library(rstan) | |
| totalC_t0 <- 7.7; # not included in data, so hard code here | |
| t0 <- 0; | |
| N_t <- 25; # calculated by inspection |
| library(tidyverse) | |
| # x <- read_csv('C:/Users/David/Downloads/Untitled spreadsheet - Sheet1.csv') | |
| # | |
| # colnames(x) | |
| # dim(x) | |
| # | |
| # xx <- x %>% | |
| # rename(organ = `Plant tissue`, | |
| # soil = `Soil \n Concentration`, | |
| # bcf = BCF) %>% |
| select extract(year from created_at) as year, container_type, count(*) as n from dbfiles where id between 1000000000 and 2000000000 group by container_type, year order by container_type, year; | |
| select created_user_id, container_type, count(*) as n from dbfiles where id between 1000000000 and 2000000000 group by container_type, created_user_id order by n desc; | |
| select * from dbfiles where created_user_id is not null; | |
| select extract(year from created_at) as year, created_user_id, container_type, count(*) as n from dbfiles where id between 9000000000 and 10000000000 group by container_type, created_user_id, year order by year, container_type, created_user_id; | |
| select null as year, created_user_id, container_type, count(*) as n from dbfiles where id between 9000000000 and 10000000000 group by container_type, created_user_id order by container_type, created_user_id; |
| "site_id","sitename","lon","lat","format_name","file_path","filename","start_date","end_date","duration","created_at" | |
| "1000026939","Moody AFB","-83.1753","30.984401","ed.met_driver_header files format","/projectnb/dietzelab/mccabete/test_pecan/cogongrass_projections/GFDL/moody_AFB/only_co2/ED_driver/Ed_driver/","Cmip5_RCP8.5_Present_day_temp","1/1/2006 06:00:00","1/1/2100 05:59:00","93 years 11 mons 30 days 23:59:00","6/4/2022 18:19:38.277567" | |
| "1000026939","Moody AFB","-83.1753","30.984401","ed.met_driver_header files format","/projectnb/dietzelab/mccabete/test_pecan/cogongrass_projections/GFDL/moody_AFB/with_co2/ED_driver/","CMIP5_RCP8.5_with_Co2","1/1/2006 06:00:00","13/12/2100 05:59:00","94 years 11 mons 11 days 23:59:00","6/4/2022 18:17:08.145333" | |
| "1000026939","Moody AFB","-83.1753","30.984401","ed.met_driver_header files format","/projectnb/dietzelab/mccabete/test_pecan/cogongrass_projections/GFDL/moody_AFB/resampled_present_day/ED_driver","Cmip5_Present_day","1/1/2006 06:00:00","1/1/2100 05:59:00","93 y |
| library(traits) | |
| library(dplyr) | |
| library(ggplot2) | |
| options(betydb_url = 'https://www.betydb.org/', | |
| betydb_api_version = 'v1' | |
| ) | |
| yields <- betydb_search(result_type = 'yields', genus = 'Panicum', limit = 'none') | |
| treatments <- betydb_query(table = 'treatments', limit = 'none') %>% | |
| dplyr::mutate(treatment_id = id) %>% |