README.md
In bheavner/minid: Working with the BD2K Minimal Viable Identifier
NOTE: lots of development has happened with minids. This package and repo is likely obsolete
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minidtools
An R API client for the
minid server. There's a
python client, too.
A minid (Minimal Viable Identifier) is an identifier that is sufficiently
simple to make creation and use trivial, while still having enough substance to
make data easily findable, accessible, interoperable, and reusable (FAIR).
Minids look like this: ark:/57799/b9j69h or this: minid:b9j69h.
minidtools provides functions for working with minids from an R session.
The package includes lookup/resolution tools, as well as functions to mint and
revise minids.
With minidtools, you can get the metadata associated with a minid, including
resolving locations for the digital object a minid identifies.
Installation
You can install minidtools from github with:
# install.packages("devtools")
devtools::install_github("bheavner/minidtools")
Quick Usage
Resolve Minid
- Get all metadata for minid
lookup("minid:b94t3q")
- Or just get location of digital object from a minid
get_location("minid:b94t3q")
Register User
config <- configuration()
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see https://orcid.org/
register(config)
# check email to get code, then add it to the config object
code(config) <- "0000000-0000-0000-0000-000000000000"
save_configuration(config)
Load Configuration from file
config <- load_configuration()
Mint Minid
mint(minid = "./someFile.RDa", config)
Edit Minid
update(id = "ark:/99999/fk4q53tj2m",
config = config,
new_title = "A Better Title!",
new_location="http://example.com/bar.txt",
new_status = "TOMBSTONE",
new_obsoleted_by = "ark:/99999/fk48s5xs8m")
Expanded Usage
Resolution and lookup functions
- Get title of digital object from minid
get_title("ark:/57799/b9j69h")
- Get newer minid for minids that have
status = TOMBSTONE
get_newer("minid:b94t3q")
- get minid for file that has an identifier (e.g. a file you've downloaded after
resolving a minid)
lookup("file:./somefile.RDa", algo = "sha256")
- Retrieve all metadata for a minid or local file that has been registered
my_minid <- lookup(query = "ark:/57799/b9j69h",
server = "http://minid.bd2k.org/minid")
my_minid <- lookup(query = "minid:b9j69h",
server = "http://minid.bd2k.org/minid")
my_minid <- lookup(query = "file:./some/file.RDa",
algo = "md5",
server = "http://minid.bd2k.org/minid")
# or, if configuration file has been loaded
my_minid <- lookup(query = "ark:/57799/b9j69h",
server = server(configuration))
- show all metadata for minid
my_minid
- Get list of locations for digitial object from metadata
locations(my_minid)
- Get other metadata values from metadata
identifier(my_minid)
short_identifier(my_minid)
checksum(my_minid)
titles(my_minid) # returns named list with created, creator, title
locations(my_minid) # returns named list with created, creator, link, uri
status(my_minid) # ACTIVE or TOMBSTONED
obsoleted_by(my_minid) # returns list
content_key(my_minid)
creator(my_minid)
orcid(my_minid)
created(my_minid)
checksum_function(my_minid)
- Get nth (default first) location of digital object from a minid or metadata
get_location(minid = "minid:b94t3q")
get_location(minid = "ark:/57799/b9j69h", n = 1,
server = "http://minid.bd2k.org/minid")
get_location(minid = "minid:b94t3q", n = 1, server = server(configuration))
get_location(my_minid)
- Get nth (default first) title of digital object from minid or metadata
get_title(minid = "minid:b94t3q")
get_title(minid = "ark:/57799/b9j69h", n = 1,
server = "http://minid.bd2k.org/minid")
get_title(minid = "minid:b94t3q", n = 1, server = server(configuration))
get_title(my_minid)
- Get nth (default first) newer minid for minids that have status = TOMBSTONED
(returns current ID if status = ACTIVE)
get_newer(minid = "minid:b94t3q")
get_newer(minid = "ark:/57799/b9j69h", n = 1,
server = "http://minid.bd2k.org/minid")
get_newer(minid = "minid:b94t3q", n = 1, server = server(configuration))
get_newer(my_minid)
User registration and configuration
Before using the minid API to mint or edit minids, you need to validate
your email address. You can do this with the register() function. When you
register, the minid server will send a unique code to your email address. You
must present this code along with your email address when minting or updating
minids.
The register() function takes a configuration object as it's argument.
Users can build a configuration object manually, e.g.
config <- configuration()
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see https://orcid.org/
As a convenience, users can also save the configuration object (including the
registration code, specified with code(config)) in a minid configuration file.
The minid configuration file can be formatted either as a python config-style or
JSON config file (default paths are ~/.minid/minid-config.cfg and
~/.minid/minid-config.json, respectively.)
These files look like this:
minid-config.cfg:
[general]
minid_server: http://minid.bd2k.org/minid
user: <Name>
email: <Email>
orcid: <optional Orcid>
code: <Code>
minid-config.json
{
"default": {
"minid_server": "http://minid.bd2k.org/minid",
"username": "<Name>",
"email": "<Email>",
"orcid": "<optional Orcid>",
"code": "<Code>"
}
}
- Create a blank configuration object and add values
config <- configuration()
server(config) <- "http://minid.bd2k.org/minid"
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see orcid.org
code(config) <- <Code>
- save a configuration object to file
save_configuration(config,
config_path = "~/.minid/minid-config.json")
save_configuration(config,
config_path = "~/.minid/minid-config.cfg",
python_style = TRUE)
- load a configuration file
config <- load_configuration(config_file = "~/.minid/minid-config.json")
- get server from configuration object
server(config)
- get other fields from configuration object
user(config)
email(config)
orcid(config)
code(config)
Creating minids
- mint minid from a file path (note: will need to add location(s) subsequently)
config <- load_configuration()
mint(minid = "./a_file.RDa", configuration = config, test = TRUE)
- mint minid from configuration and minid objects
# set up new configuration object
config <- configuration()
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see http://orch.id
code(config) <- "00000000-0000-0000-0000-000000000000" # see register()
# set up minid object
new_minid <- minid()
checksum_function(new_minid) <- "sha256"
checksum(new_minid) <- digest::digest("./somefile.RDa",
file = TRUE,
algo = "sha256")
titles(new_minid) <- list(title = "An Example Object Title")
locations(new_minid) <- list(link = "http://example.com/somefile.RDa") # optional
# mint the new minid
mint(minid = new_minid, configuration = config, test = TRUE)
- mint minid from named lists
computed_checksum <- digest::digest("./somefile.RDa",
file = TRUE,
algo = "sha256")
new_minid = list(
checksum_function = "sha256",
checksum = computed_checksum,
titles = "An Example Object Title",
locations = "http://example.com/somefile.RDa")
configuration = list(
server = "http://minid.bd2k.org/minid",
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000", # see http://orch.id
code(config) <- "00000000-0000-0000-0000-000000000000" # see register()
)
minted <- mint(minid = new_minid, configuration = config, test = TRUE)
or
minid_list <- as.list(minid)
config_list <- as.list(config)
minted <- mint(minid = minid_list, configuration = config_list, test = TRUE)
Revising minids
update(id = "ark:/99999/fk4q53tj2m",
config = config,
new_title = "A Better Title!",
new_location="http://example.com/bar.txt",
new_status = "TOMBSTONE",
new_obsoleted_by = "ark:/99999/fk48s5xs8m")
More information
More information about the project can be found at:
http://minid.bd2k.org/
bheavner/minid documentation built on Aug. 1, 2020, 9:38 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
NOTE: lots of development has happened with minids. This package and repo is likely obsolete
| Service | Master | Develop |
|:-------------:|:------:|:-------:|
| CI Status | | |
| Test Coverage | | |
minidtools
An R API client for the minid server. There's a python client, too.
A minid (Minimal Viable Identifier) is an identifier that is sufficiently
simple to make creation and use trivial, while still having enough substance to
make data easily findable, accessible, interoperable, and reusable (FAIR).
Minids look like this: ark:/57799/b9j69h or this: minid:b9j69h.
minidtools provides functions for working with minids from an R session.
The package includes lookup/resolution tools, as well as functions to mint and
revise minids.
With minidtools, you can get the metadata associated with a minid, including
resolving locations for the digital object a minid identifies.
Installation
You can install minidtools from github with:
# install.packages("devtools")
devtools::install_github("bheavner/minidtools")
Quick Usage
Resolve Minid
- Get all metadata for minid
lookup("minid:b94t3q")
- Or just get location of digital object from a minid
get_location("minid:b94t3q")
Register User
config <- configuration()
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see https://orcid.org/
register(config)
# check email to get code, then add it to the config object
code(config) <- "0000000-0000-0000-0000-000000000000"
save_configuration(config)
Load Configuration from file
config <- load_configuration()
Mint Minid
mint(minid = "./someFile.RDa", config)
Edit Minid
update(id = "ark:/99999/fk4q53tj2m",
config = config,
new_title = "A Better Title!",
new_location="http://example.com/bar.txt",
new_status = "TOMBSTONE",
new_obsoleted_by = "ark:/99999/fk48s5xs8m")
Expanded Usage
Resolution and lookup functions
- Get title of digital object from minid
get_title("ark:/57799/b9j69h")
- Get newer minid for minids that have
status = TOMBSTONE
get_newer("minid:b94t3q")
- get minid for file that has an identifier (e.g. a file you've downloaded after resolving a minid)
lookup("file:./somefile.RDa", algo = "sha256")
- Retrieve all metadata for a minid or local file that has been registered
my_minid <- lookup(query = "ark:/57799/b9j69h",
server = "http://minid.bd2k.org/minid")
my_minid <- lookup(query = "minid:b9j69h",
server = "http://minid.bd2k.org/minid")
my_minid <- lookup(query = "file:./some/file.RDa",
algo = "md5",
server = "http://minid.bd2k.org/minid")
# or, if configuration file has been loaded
my_minid <- lookup(query = "ark:/57799/b9j69h",
server = server(configuration))
- show all metadata for minid
my_minid
- Get list of locations for digitial object from metadata
locations(my_minid)
- Get other metadata values from metadata
identifier(my_minid)
short_identifier(my_minid)
checksum(my_minid)
titles(my_minid) # returns named list with created, creator, title
locations(my_minid) # returns named list with created, creator, link, uri
status(my_minid) # ACTIVE or TOMBSTONED
obsoleted_by(my_minid) # returns list
content_key(my_minid)
creator(my_minid)
orcid(my_minid)
created(my_minid)
checksum_function(my_minid)
- Get nth (default first) location of digital object from a minid or metadata
get_location(minid = "minid:b94t3q")
get_location(minid = "ark:/57799/b9j69h", n = 1,
server = "http://minid.bd2k.org/minid")
get_location(minid = "minid:b94t3q", n = 1, server = server(configuration))
get_location(my_minid)
- Get nth (default first) title of digital object from minid or metadata
get_title(minid = "minid:b94t3q")
get_title(minid = "ark:/57799/b9j69h", n = 1,
server = "http://minid.bd2k.org/minid")
get_title(minid = "minid:b94t3q", n = 1, server = server(configuration))
get_title(my_minid)
- Get nth (default first) newer minid for minids that have status = TOMBSTONED (returns current ID if status = ACTIVE)
get_newer(minid = "minid:b94t3q")
get_newer(minid = "ark:/57799/b9j69h", n = 1,
server = "http://minid.bd2k.org/minid")
get_newer(minid = "minid:b94t3q", n = 1, server = server(configuration))
get_newer(my_minid)
User registration and configuration
Before using the minid API to mint or edit minids, you need to validate
your email address. You can do this with the register() function. When you
register, the minid server will send a unique code to your email address. You
must present this code along with your email address when minting or updating
minids.
The register() function takes a configuration object as it's argument.
Users can build a configuration object manually, e.g.
config <- configuration()
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see https://orcid.org/
As a convenience, users can also save the configuration object (including the
registration code, specified with code(config)) in a minid configuration file.
The minid configuration file can be formatted either as a python config-style or
JSON config file (default paths are ~/.minid/minid-config.cfg and
~/.minid/minid-config.json, respectively.)
These files look like this:
minid-config.cfg:
[general]
minid_server: http://minid.bd2k.org/minid
user: <Name>
email: <Email>
orcid: <optional Orcid>
code: <Code>
minid-config.json
{
"default": {
"minid_server": "http://minid.bd2k.org/minid",
"username": "<Name>",
"email": "<Email>",
"orcid": "<optional Orcid>",
"code": "<Code>"
}
}
- Create a blank configuration object and add values
config <- configuration()
server(config) <- "http://minid.bd2k.org/minid"
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see orcid.org
code(config) <- <Code>
- save a configuration object to file
save_configuration(config,
config_path = "~/.minid/minid-config.json")
save_configuration(config,
config_path = "~/.minid/minid-config.cfg",
python_style = TRUE)
- load a configuration file
config <- load_configuration(config_file = "~/.minid/minid-config.json")
- get server from configuration object
server(config)
- get other fields from configuration object
user(config)
email(config)
orcid(config)
code(config)
Creating minids
- mint minid from a file path (note: will need to add location(s) subsequently)
config <- load_configuration()
mint(minid = "./a_file.RDa", configuration = config, test = TRUE)
- mint minid from configuration and minid objects
# set up new configuration object
config <- configuration()
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000" # see http://orch.id
code(config) <- "00000000-0000-0000-0000-000000000000" # see register()
# set up minid object
new_minid <- minid()
checksum_function(new_minid) <- "sha256"
checksum(new_minid) <- digest::digest("./somefile.RDa",
file = TRUE,
algo = "sha256")
titles(new_minid) <- list(title = "An Example Object Title")
locations(new_minid) <- list(link = "http://example.com/somefile.RDa") # optional
# mint the new minid
mint(minid = new_minid, configuration = config, test = TRUE)
- mint minid from named lists
computed_checksum <- digest::digest("./somefile.RDa",
file = TRUE,
algo = "sha256")
new_minid = list(
checksum_function = "sha256",
checksum = computed_checksum,
titles = "An Example Object Title",
locations = "http://example.com/somefile.RDa")
configuration = list(
server = "http://minid.bd2k.org/minid",
user(config) <- "Jane Example"
email(config) <- "jexample@example.com"
orcid(config) <- "0000-0000-0000-0000", # see http://orch.id
code(config) <- "00000000-0000-0000-0000-000000000000" # see register()
)
minted <- mint(minid = new_minid, configuration = config, test = TRUE)
or
minid_list <- as.list(minid)
config_list <- as.list(config)
minted <- mint(minid = minid_list, configuration = config_list, test = TRUE)
Revising minids
update(id = "ark:/99999/fk4q53tj2m",
config = config,
new_title = "A Better Title!",
new_location="http://example.com/bar.txt",
new_status = "TOMBSTONE",
new_obsoleted_by = "ark:/99999/fk48s5xs8m")
More information
More information about the project can be found at: http://minid.bd2k.org/
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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