Convert trainings to use datapack and dataone

[laijasmine]

Convert the datateam workflow to use datapack and dataone

Essential usage changes

• [x] Chapter 2 Creating a new data package
• [x] Chapter 4.14 - arcticdatautils::publish_update -> datapack::uploadPackage
• [x] Chapter 5 - updating a package

Other

• [x] Adding file hierarchy (adding a targetPath)
• [x] Instructions for nesting datasets (might need to continue using arcticdatautils)
• [x] Should standardize language used to make it easier for first time learners. For example - make sure the way we are calling things are consistent in the Prov chapter
• [ ] Put in PRs in datapack and dataone to make the help documentation more descriptive

packageId <- "resource_map_urn:uuid:14908960-856a-4511-b4a0-8b596a31a3b8"
dp <- getDataPackage(d1c, identifier=packageId, lazyLoad=TRUE, quiet=FALSE)

#remove the zip files
zipId <- selectMember(dp, name="sysmeta@formatId", value="application/vnd.shp+zip")
removeMember(dp, zipId, removeRelationships = T)
metadataId <- selectMember(dp, name="sysmeta@formatId", value="https://eml.ecoinformatics.org/eml-2.2.0")

#add an existing data object
dataObj <- getDataObject(d1c, id="urn:uuid:48d36037-5fbb-4191-951e-4035f8f07cd1", lazyLoad=T, limit="1TB")
dp <- addMember(dp, dataObj, mo=metadataId)
myAccessRules <- data.frame(subject="http://orcid.org/0000-0001-8888-547X", permission="changePermission") 
packageId <- uploadDataPackage(d1c, dp, public=TRUE, accessRules=myAccessRules, quiet=FALSE)

[laijasmine]

To do before the datapack dataone workflow can be fully implemented:

• [x] Create the Rmarkdown files in a separate section
• [x] Merge with current book
• [x] Have interns review the new files

[laijasmine]

• [x] Add some instructions to add admin account to access policy - "CN=arctic-data-admins,DC=dataone,DC=org"
• [x] Remove this section : ... you can change the use_doi argument to TRUE. ...

[laijasmine]

• [x] add info box on getting metadataId for other eml versions, or any eml version
• metadataId <- selectMember(dp, name="sysmeta@formatId", value="https://eml.ecoinformatics.org/eml-2.2.0")
• [x] add block for place holder for EML edits before write_eml instructions
• [x] add instructions for reading eml doc <- read_eml(getObject(d1c@mn, metadataId))

[laijasmine]

update sections that have the node argument (mainly in arcticdatautils and dataone functions)

d1c@mn is equivalent to using adc; for example:

doc <- read_eml(getObject(d1c@mn, metadataId))

[laijasmine]

For the workflow to be used in the trainings

• [x] create separate branch for the datapack dataone rewrite
• [x] overhaul contents of chapter 2
• [x] adjust the nodes for chapter 3 & 4
• [ ] make it clear where arcticdatautils is being used

[laijasmine]

• [ ] add example for adding large number of files based on a folder

[laijasmine]

make sure datafiles are public after publishing the dataset? seems to not happen in some cases... need to investigate further. Seems to be related to uploading data files through R first.