Merge pull request #1 from eco4cast/usgs_challenge_details

USGS Challenge Details

.github/workflows/targets.yaml

@@ -8,7 +8,7 @@ on:
 name: target-generation
 
 jobs:
-  phenology:
+  chl-targets:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -23,44 +23,7 @@ jobs:
       - name: Generate targets
         shell: Rscript {0}
         run: |
-          install.packages("RCurl")
-          source("targets/phenology_targets.R")
-
-  beetles:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_SUBMISSIONS }}
-      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_SUBMISSIONS }}
-      OSN_KEY: ${{ secrets.OSN_KEY }}
-      OSN_SECRET: ${{ secrets.OSN_SECRET }}
-      NEON_TOKEN: ${{ secrets.NEON_TOKEN }}
-    container: rocker/geospatial:latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Generate targets
-        shell: Rscript {0}
-        run: |
-          install.packages(c("neonstore","RCurl","duckdbfs","ISOweek"))
-          source("targets/beetles_targets.R")
-
-  ticks:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_SUBMISSIONS }}
-      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_SUBMISSIONS }}
-      OSN_KEY: ${{ secrets.OSN_KEY }}
-      OSN_SECRET: ${{ secrets.OSN_SECRET }}
-      NEON_TOKEN: ${{ secrets.NEON_TOKEN }}
-    container: rocker/geospatial:latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Generate targets
-        shell: Rscript {0}
-        run: |
-          install.packages(c("neonstore","RCurl","duckdbfs","ISOweek"))
-          source("targets/ticks_targets.R")
+          install.packages(c("clustermq", "dataRetrieval", "RCurl", "tarchetypes", "targets"))
+          setwd("targets")
+          targets::tar_make()
 

.gitignore

@@ -62,3 +62,9 @@ archive/
 .DS_Store
 *.gz
 *.csv
+
+**/out/**
+
+**/in/**
+
+_targets/

DESCRIPTION

@@ -1,11 +1,16 @@
-Package: neon4cast-ci
-Title: Cyberinfrastructure for the VERA Forecasting Challenge
+Package: usgsrc4cast-ci
+Title: Cyberinfrastructure for the EFI-USGS River Chlorophyll Forecasting Challenge
 Version: 0.1
 Authors@R: c(person(
               "Quinn", "Thomas", 
               email = "[email protected]", 
               role = c("aut", "cre"),
-              comment = c(ORCID = "0000-0003-1282-7825")))
+              comment = c(ORCID = "0000-0003-1282-7825")),
+              person(
+              "Jacob", "Zwart", 
+              email = "[email protected]", 
+              role = c("aut", "cre"),
+              comment = c(ORCID = "0000-0002-3870-405X")))
 Description: Cyberinfrastructure that processing submissions, scores submissions, generates catalog, and generates dashboards
 License: MIT
 Encoding: UTF-8

R/access_model_metadata.R

@@ -1,4 +1,4 @@
-s3 <- arrow::s3_bucket(bucket = "bio230121-bucket01/vera4cast/metadata/model_id/",
+s3 <- arrow::s3_bucket(bucket = "bio230121-bucket01/vera4cast/metadata/model_id/", # update from vera4cast?
                        endpoint_override = "renc.osn.xsede.org", anonymous = TRUE)
 
 d1 <- arrow::open_dataset(s3, format = "json") |> dplyr::collect()

README.md

@@ -1,4 +1,4 @@
-# National Ecological Observatory Network (NEON) Ecological Forecasting Challenge
+# Ecological Forecasting Initiative (EFI) and U.S. Geological Survey (USGS) River Chlorophyll Forecasting Challenge
 
 The following elements of a forecasting challenge workflow are included in this repo.  The GitHub Actions are the tool for automating the tasks.
 
@@ -12,6 +12,10 @@ The following elements of a forecasting challenge workflow are included in this
 9) Creation of Docker containers with supporting software
 10) Creation of archive/snapshots of challenge submissions and targets.
 
-See [https://doi.org/10.1002/fee.2616](https://doi.org/10.1002/fee.2616) for more information on the structure of a forecasting challenge.
+See [https://doi.org/10.1002/fee.2616](https://doi.org/10.1002/fee.2616) for more information on the structure of a forecasting challenge, using the NEON forecasting challenge as the example. 
 
 Supported by the U.S. National Science Foundation grants (DEB-1926388 and OAC-2209866)
+
+## Disclaimer
+Although this software program has been used by the U.S. Geological Survey (USGS), no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.
+This software is provided “AS IS.”

USGS_site_metadata.csv

@@ -0,0 +1,11 @@
+site_id,project_id,agency_cd,site_no,station_nm,site_tp_cd,latitude,longitude,site_url,colocated,queryTime
+USGS-14211720,usgsrc4cast,USGS,14211720,"WILLAMETTE RIVER AT PORTLAND, OR",ST-TS,45.5175,-122.6691667,https://waterdata.usgs.gov/monitoring-location/14211720,FALSE,2023-12-20T22:59:24Z
+USGS-14211010,usgsrc4cast,USGS,14211010,"CLACKAMAS RIVER NEAR OREGON CITY, OR",ST,45.3792874,-122.5773134,https://waterdata.usgs.gov/monitoring-location/14211010,FALSE,2023-12-20T22:59:24Z
+USGS-14181500,usgsrc4cast,USGS,14181500,"NORTH SANTIAM RIVER AT NIAGARA, OR",ST,44.75377778,-122.2974444,https://waterdata.usgs.gov/monitoring-location/14181500,FALSE,2023-12-20T22:59:24Z
+USGS-05586300,usgsrc4cast,USGS,05586300,"ILLINOIS RIVER AT FLORENCE, IL",ST,39.63275,-90.6076667,https://waterdata.usgs.gov/monitoring-location/05586300,FALSE,2023-12-20T22:59:24Z
+USGS-05558300,usgsrc4cast,USGS,05558300,"ILLINOIS RIVER AT HENRY, IL",ST,41.10727778,-89.3562222,https://waterdata.usgs.gov/monitoring-location/05558300,FALSE,2023-12-20T22:59:24Z
+USGS-05553700,usgsrc4cast,USGS,05553700,"ILLINOIS RIVER AT STARVED ROCK, IL",ST,41.3247564,-88.9839693,https://waterdata.usgs.gov/monitoring-location/05553700,FALSE,2023-12-20T22:59:24Z
+USGS-05543010,usgsrc4cast,USGS,05543010,"ILLINOIS RIVER AT SENECA, IL",ST,41.29988889,-88.6141944,https://waterdata.usgs.gov/monitoring-location/05543010,FALSE,2023-12-20T22:59:24Z
+USGS-05549500,usgsrc4cast,USGS,05549500,"FOX RIVER NEAR MCHENRY, IL",ST,42.3100222,-88.2514745,https://waterdata.usgs.gov/monitoring-location/05549500,FALSE,2023-12-20T22:59:24Z
+USGS-01427510,usgsrc4cast,USGS,01427510,DELAWARE RIVER AT CALLICOON NY,ST,41.75675,-75.0574167,https://waterdata.usgs.gov/monitoring-location/01427510,FALSE,2023-12-20T22:59:24Z
+USGS-01463500,usgsrc4cast,USGS,01463500,Delaware River at Trenton NJ,ST,40.22166667,-74.7780556,https://waterdata.usgs.gov/monitoring-location/01463500,FALSE,2023-12-20T22:59:24Z