helm/README.md

In DataONEorg/scythe: Harvest and register data package citations

Scythe Helm Chart

This Helm chart deploys a CronJob that does a citation search on a set of DataONE member nodes using scythe.

Search Script and Container

scripts/search.R is copied into the Dockerfile and run in the CronJob. It takes the node identifiers listed in the values.yaml file as input. DOIs (either identifiers or series identifiers) are retrieved from each node, then passed through scythe::citation_search, which searches for citations in PLOS, Springer, Scopus, and xDD. Citations already in the metrics service are removed, and the citations are written to a csv. This table can be passed to scythe::write_citation_pairs to create the JSON file needed for ingest into the metrics system.

CronJob

In values.yaml, key fields to configure are:

• cronjob.schedule: Schedule for the CronJob (in cron format).
• cronjob.nodes: A set of node identifiers to be passed to the R script, as a comma separated list
• cronjob.rows: Optional number of rows to return per node when getting DOIs. Leave empty to return all identifiers

API Keys

For instructions on obtaining an API key, see README.md at the package level.

Keys are made accessible to the deployment using Kubernetes secrets. To set API keys, run:

kubectl create secret generic -n scythe api-keys \
  --from-literal=springer={key} \
  --from-literal=scopus={key}

Persistent Storage

This Helm chart uses a dynamic PVC using CephFS to save results from the scythe run. An example configuration file is shown below. For more information on CephFS on the cluster see k8s-cluster docs.

---
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: scythe-results
spec:
  accessModes:
    - ReadWriteMany
  resources:
    requests:
      storage: 10Gi
  storageClassName: csi-cephfs-sc

To create the PVC, run kubectl apply -f pvc.yaml -n scythe. This should only be done once.

DataONEorg/scythe documentation built on June 15, 2025, 6:23 a.m.