feat: knb-lter-cap.632.13; new style config.yaml and config params

README.md

@@ -14,6 +14,12 @@ repository should be able to be ignored going forward. 'cndep' had also held
 the data, but those are all now moved to the cndep folder of the department
 drive.
 
+### knb-lter-cap.632.13 *2022-06-02*
+
+- fixing an error in the dates assigned to PRS probe blanks in the most recent deployment
+- update config.yaml to newest format
+
+
 ### knb-lter-cap.632.12 *2022-05-12*
 
 - data refresh with a focus on PRS data

config.yaml

@@ -1,9 +1,7 @@
-packageNum: 632
-packageIdent: knb-lter-cap.632.12
+scope: knb-lter-cap
+identifier: 632
 baseURL: https://data.gios.asu.edu/datasets/cap/
 project: lter
+title: 'Desert Fertilization Experiment: investigation of Sonoran desert ecosystem response to atmospheric deposition and experimental nutrient addition, ongoing since 2006'
 maintenance: regular
-title: "Desert Fertilization Experiment: investigation of Sonoran desert ecosystem response to atmospheric deposition and experimental nutrient addition, ongoing since 2006"
-geographicCoverage:
-  geographicDescription: 'CAP LTER study area: greater Phoenix, Arizona (USA) metropolitan
-    area and surrounding Sonoran desert region'
+geographic_description: 'CAP LTER study area: greater Phoenix, Arizona (USA) metropolitan area and surrounding Sonoran desert region'

knb-lter-cap.632.Rmd

@@ -870,13 +870,13 @@ if (!file.exists("config.yaml")) {
   stop("config.yaml not found")
 }
 packageIdent <- yaml::yaml.load_file("config.yaml")$packageIdent
-packageNum <- yaml::yaml.load_file("config.yaml")$packageNum
+identifier   <- yaml::yaml.load_file("config.yaml")$identifier
 ```
 
 ```{r preview_data_file_to_upload}
 
 # preview data set files that will be uploaded to S3
-list.files(pattern = paste0(packageNum, "_"))
+list.files(pattern = paste0(identifier, "_"))
 ```
 
 Move data and final xml files to respective ASU locations.
@@ -891,7 +891,7 @@ source("~/Documents/localSettings/aws.s3")
 ```{r upload_data_S3}
 
 # upload files to S3
-lapply(list.files(pattern = paste0(packageNum, "_")), gioseml::data_to_amz)
+lapply(list.files(pattern = paste0(identifier, "_")), gioseml::data_to_amz)
 ```
 
 
@@ -913,8 +913,8 @@ EDIutils::login(
 ```{r edi-evaluate, eval=TRUE, echo=TRUE, message=TRUE}
 
 evaluation <- EDIutils::evaluate_data_package(
-  eml         = paste0(packageIdent, ".xml"),
-  useChecksum = TRUE,
+  eml         = paste0(eml[["packageId"]], ".xml"),
+  useChecksum = FALSE,
   env         = "staging"
 )
 
@@ -950,7 +950,7 @@ if (eval_status) {
 ```{r edi-update, eval=TRUE, echo=TRUE, message=TRUE}
 
 EDIutils::update_data_package(
-  eml         = paste0(packageIdent, ".xml"),
+  eml         = paste0(eml[["packageId"]], ".xml"),
   useChecksum = TRUE,
   env         = "production"
 )
@@ -972,7 +972,7 @@ remove data files (if desired)
 
 ```{r delete-data-files}
 
-dataFilesToRemove <- dir(pattern = paste0(packageNum, "_"))
+dataFilesToRemove <- dir(pattern = paste0(identifier, "_"))
 file.remove(dataFilesToRemove)
 ```
 

taxonomicCoverage.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" packageId="90c63636-f21a-4052-8949-74406cc74c7e" system="uuid" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0 https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd">
+<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" packageId="3a51dc87-0461-4b40-b94e-aed0c0708117" system="uuid" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0 https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd">
   <taxonomicClassification>
     <taxonRankName>kingdom</taxonRankName>
     <taxonRankValue>Plantae</taxonRankValue>