Pubmetric RESTful API

Introduction … . Once the RESTful API is up and running it automatically regenerates the co-citation graph on a monthly basis.

Setup

Index

Score workflows

Endpoint: POST /score_workflow

Calculates the workflow_average and the tool_average metric using the latest co-citation graph, and an uploaded CWL file. Generates benchmarks for the metric scores as well as the ages of tools.

• Parameters:

  • cwl_file (File): A CWL file containing the workflow

• Success Response:

  • Code: 200

  • Content: application/ json containing metric and age benchmarks.

Recreate Graph

Endpoint: POST /recreate_graph

Regenerates the co-citation graph on demand.

• Parameters:

  • topic_id (string|None): The topic ID from which tools are downloaded, or None for full bio.tools.

  • tool_selection (string|None): Premade lists of annotated tools, “full” for all well annotated tools, “workflomics” for tools present in workflomics. Or, a user specified list of tools (bio.tools tool names) which will be used to generate the graph.

  • inpath (string|None): The directory from which an old metadata file should be loaded. Usually not used, as it does not download potential new additions to bio.tools.

• Success Response:

  • Code: 200

  • Content: “Graph and metadata file recreated successfully!”