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Switch from EML to eml2 in publishing-data lesson #23

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dd6e8c2
Switch from `EML` to `eml2`
cboettig Apr 18, 2018
a31cd32
fix typo
cboettig Apr 18, 2018
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39 changes: 25 additions & 14 deletions publishing-data/upload-data.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -33,22 +33,23 @@ Once you are logged in, navigate to your Profile Settings, and locate the "Authe
Next, modify the metadata file associated with the package to set yourself as the owner. This will help us differentiate the test data later. Open the `strix-pacific-northwest.xml` file in RStudio, and change the `givenName` and `surName` fields at the top to your name.

```{r}
library(EML)
# devtools::install_github("NCEAS/arcticdatautils")
library(arcticdatautils)

# devtools::install_github("cboettig/eml2")
library(eml2)

# Load the EML file into R
emlFile <- "strix-pacific-northwest.xml"
doc <- read_eml(emlFile)

# Change creator to us
doc@dataset@creator <- c(eml_creator("Matthew", "Jones", email = "[email protected]"))
doc$dataset$creator <- set_responsibleParty("Matthew", "Jones", email = "[email protected]")

# Change abstract to the better one we wrote
doc@dataset@abstract <- as(set_TextType("better-abstract.md"), "abstract")
doc$dataset$abstract <- set_TextType("better-abstract.md")

# Save it back to the filesystem
write_eml(doc, "strix-pacific-northwest.xml")
eml_validate("strix-pacific-northwest.xml")
```

## Uploading A Package Using `uploadDataPackage`
Expand All @@ -75,19 +76,29 @@ We then add a metadata file, data file, R script and output data file to this pa
sourceId <- paste0("urn:uuid:", uuid::UUIDgenerate())
progId <- paste0("urn:uuid:", uuid::UUIDgenerate())
outputId <- paste0("urn:uuid:", uuid::UUIDgenerate())
doc@dataset@otherEntity[[1]]@id <- new("xml_attribute", sourceId)
doc@dataset@otherEntity[[2]]@id <- new("xml_attribute", progId)
doc@dataset@otherEntity[[3]]@id <- new("xml_attribute", outputId)
doc$dataset$otherEntity[[1]]$id <- sourceId
doc$dataset$otherEntity[[2]]$id <- progId
doc$dataset$otherEntity[[3]]$id <- outputId
```

```{r}
repo_obj_service <- paste0(d1c@mn@endpoint, "/object/")
doc@dataset@otherEntity[[1]]@physical[[1]]@distribution[[1]]@online@url <-
new("url", paste0(repo_obj_service, sourceId))
doc@dataset@otherEntity[[2]]@physical[[1]]@distribution[[1]]@online@url <-
new("url", paste0(repo_obj_service, progId))
doc@dataset@otherEntity[[3]]@physical[[1]]@distribution[[1]]@online@url <-
new("url", paste0(repo_obj_service, outputId))

doc$dataset$otherEntity[[1]]$physical$distribution$online$url <-
paste0(repo_obj_service, sourceId)

doc$dataset$otherEntity[[2]]$physical$distribution$online$url <-
paste0(repo_obj_service, progId)

doc$dataset$otherEntity[[3]]$physical$distribution$online$url <-
paste0(repo_obj_service, outputId)

write_eml(doc, "strix-pacific-northwest.xml")
eml_validate("strix-pacific-northwest.xml")
```


```{r}
# Add the metadata document to the package
metadataObj <- new("DataObject",
format="eml://ecoinformatics.org/eml-2.1.1",
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