UNIX Command-Line (CLI)
Java Command Line Interface
This is the documentation of the java cli of nanopub.java.
Available Commands
You can get the list of commands by typing:
java -jar nanopub-<version>-jar-with-dependencies.jar
In the following list you can see the short command first, followed by the classname implementing that command.
- check / CheckNanopub
- get / GetNanopub
- publish / PublishNanopub
- sign / SignNanopub
- mktrusty / MakeTrustyNanopub
- fix / FixTrustyNanopub
- status / NanopubStatus
- server / GetServerInfo
- mkindex / MakeIndex
- mkkeys / MakeKeys
- html / Nanopub2Html
- now / TimestampNow
- op / Run
- setting / ShowSetting
- query / RunQuery
- udtime / TimestampUpdater
- strip / StripDown
- shacl / ShaclValidator
- rocrate / RoCrateImporter
Some commands are grouped as subcommands of the op
command.
- filter / Filter
- extract / Extract
- gml / Gml
- fingerprint / Fingerprint
- topic / Topic
- reuse / Reuse
- count / Count
- decontext / Decontextualize
- union / Union
- ireuse / IndexReuse
- exportjson / ExportJson
- namespaces / Namespaces
- aggregate / Aggregate
- import / Import
- create / Create
- build / Build
- tar / Tar
To get more information on the usage of a command just type it in. E.g.
java -jar nanopub-<version>-jar-with-dependencies.jar check
will output:
Usage: <main class> [options] input-nanopubs
Options:
-s
Load nanopubs from given SPARQL endpoint
-v
Verbose
Default: false
Keys and Profile
Some commands use the keys in ~/.nanopub/
. To generate the key pair use:
java -jar nanopub-<version>-jar-with-dependencies.jar mkkeys
The command sign
takes a profile file in yaml format:
profile.yaml
orcid_id: https://orcid.org/0009-0008-3635-347X
public_key: /Users/name/.nanopub/id_rsa.pub
private_key: /Users/name/.nanopub/id_rsa
Shacl Validation
Usage: java -jar nanopub.jar shacl [options]
Options:
* -n
nanopub-to-be-validated
* -s
SHACL shape file
The command takes two files in the .trig format, the nanopublication and the SHACL specification or shape file. This shape-file corresponds to the profile in handle-based FDOs.