Examples¶
Note
Use the Arrow Up and Arrow Down keys to find commands in the command history. These can then be edited and run again.
Viewing and manipulating the session variables¶
Viewing and manipulating the session variables used when performing operations against the DataONE infrastructure via the DataONE Command Line Interface (CLI).
If desired, the session variables can be reset back to their defaults (useful if they were modified by an existing .dataone_cli.conf
file at startup):
> reset
Set the authentication session variables for authenticated access using a certificate from CILogon (downloaded to the default location in /tmp):
> set anonymous false
> set cert-file none
> set key-file none
Or set to use a certificate in a non-standard location:
> set cert-file /etc/dataone/client/certs/myclientcert.pem
View all the session variables:
> set
Save the session variables to a file for later use:
> save ~/d1/mysettings
Exit the CLI:
> exit
Searching for Science Data¶
A scientist can discover and download Science Data to leverage them in their own research.
Load the session variables from the file created in the previous step:
> load ~/d1/mysettings
View the session variables:
> set
Perform an unlimited search:
> set query *:*
> search
Restrict the search to a specific time or later:
> set from-date 1998-01-01T05:00:00
> search
Modify the search parameters to find only Science Data that originated from the “DEMO3” MN and search:
> set query origin_mn:DEMO3
> search
The search terms can also be specified after the “search” command:
> search barnacle
Modify the search parameters to find only Science Data that are of type text/csv and search again:
> set format-id text/csv
> search barnacle
Downloading Science Data Objects¶
View the session variables:
> set
Set MN from which to download the Science Data Object:
> set mn-url https://dataone.member.node.com/mn/
Download Science Data Object and save to local file:
> get hdl:10255/dryad.669/mets.xml ~/my_dataone_files/dryad669.xml
Downloading System Metadata¶
System Metadata is an XML document that contains additional information about a Science Data Object.
Retrieve the System Metadata and display it:
> meta hdl:10255/dryad.669/mets.xml
Retrieve the System Metadata and save it to a file:
> meta hdl:10255/dryad.669/mets.xml ~/d1/dryad669_system_metadata.xml
Downloading an access restricted object¶
Authenticate with CILogon, at https://cilogon.org/?skin=DataONE
Tell the CLI that you wish to use authentication:
> set anonymous False
Download an object for which you have read access:
> get my-access-controlled-identifier
See Authentication for more information.
Uploading Science Data Objects¶
A scientist can upload a set of Science Data to benefit from the services provided by DataONE.
Select MN to which to upload the Science Data Object:
> set mn-url https://dataone.member.node.com/mn/
Configure the session variables used when generating System Metadata:
> set rights-holder CN=MATTJTEMP,DC=dataone,DC=org
> set origin-mn DEMO1
> set authoritative-mn DEMO1
Create an Access Policy that has only public read permisisons:
> clearaccess
> allowaccess public read
Add a create (upload) operation of the Science Data Object to the write operation queue:
> create mynewpid ~/path/to/my/file
View the queue:
> queue
Edit the queue if there are any mistakes in the create operation:
> edit
Perform all operations in the queue:
> run
Store the settings in .dataone_cli.conf
for use when creating similar Science Data Objects later:
> save
Exit the CLI:
> exit
Misc operations¶
Find replicas of Science Data Objects:
> resolve hdl:10255/dryad.669/mets.xml
Display list of Science Data Objects on a MN or CN:
> set mn-url https://mn.dataone.org/mn
> set start 100
> set count 10
> list
Display event log on a MN:
> reset
> set anonymous false
> set cert-file /etc/dataone/client/certs/myclientcert.pem
> set key-file None
> set mn-url https://dataone.org/mn
> log
Download the event log and save it to a file:
> log events.xml