Refactor to be compatible with new version of EML (eml2)

[jeanetteclark]

The EML update moving to S3 objects is coming, and while it does maintain backwards compatibility with the old version, I'd like to see us refactor our code to stay up to date. We'll need to update all of the functions that rely on eml. Here is a running list (from eml.R, there may be others). We will also need to update the tests.

• [x] add_methods_step : function (doc, title, description)
• [x] clear_methods : function (doc)
• [x] eml_abstract : function (text)
• [x] eml_add_entities : function (doc, entities, resolve_base = "https://cn.dataone.org/cn/v2/resolve/")
• [x] eml_address : function (delivery_points, city, administrative_area, postal_code)
• [x] eml_associated_party : function (...)
• [x] eml_contact : function (...)
• [x] eml_creator : function (...)
• [x] eml_geographic_coverage : function (description, north, east, south, west)
• [x] eml_individual_name : function (given_names = NULL, sur_name)
• [x] eml_metadata_provider : function (...)
• [x] eml_otherEntity_to_dataTable : function (eml, otherEntity, validate_eml = TRUE)
• [x] eml_party : function (type = "associatedParty", given_names = NULL, sur_name = NULL, organization = NULL, position = NULL, email = NULL, phone = NULL, address = NULL, userId = NULL, role = NULL)
• [x] eml_project : function (title, personnelList, abstract = NULL, funding = NULL, studyAreaDescription = NULL, designDescription = NULL, relatedProject = NULL)
• [x] eml_set_reference : function (element_to_reference, element_to_replace)
• [x] eml_validate_attributes : function (attributes)
• [x] get_doc_id : function (sysmeta)
• [x] pid_to_eml_entity : function (mn, pid, entityType = "otherEntity", ...)
• [x] pid_to_eml_physical : function (mn, pids)
• [x] set_abstract : function (doc, text)
• [x] sysmeta_to_eml_physical : function (sysmeta)
• [x] which_in_eml : function (eml_list, element, test)

I created a new branch called eml2_refactor where we can push these changes

[jeanetteclark]

I've been slowly chipping away at this. Two things came up today:

• using the c() function to group EML elements created by helpers (like eml_creator, or even EML::set_physical) mangles them, need to make sure that this is shown clearly in the docs where needed

• the stopifnot tests used when an argument is expected to be a certain type of EML element (such as a list of personnel) don't work anymore because class(...) returns list for everything. Need to think about which of these tests are necessary and how to write them, probably as mini-validation functions

[jeanetteclark]

done with all of the functions, and have done some preliminary testing. so far so good! tasks remaining:

• [x] review documentation to make sure dontrun examples would run

• [x] identify places where stopifnot tests should be implemented

• [x] fix warnings and notes after checking the package with devtools