10. Variable Expansion

Pegasus Planner supports notion of variable expansions in the Abstract Workflow and the catalog files along the same lines as bash variable expansion works. This is often useful, when you want paths in your catalogs or profile values in the abstract workflow to be picked up from the environment. An error is thrown if a variable cannot be expanded.

To specify a variable that needs to be expanded, the syntax is ${VARIABLE_NAME} , similar to BASH variable expansion. An important thing to note is that the variable names need to be enclosed in curly braces. For example

${FOO}  - will be expanded by Pegasus
$FOO    - will NOT be expanded by Pegasus.

Also variable names are case sensitive.

Some examples of variable expansion are illustrated below:

• Abstract Workflow

  A job in the workflow file needs to have a globus profile key project associated and the value has to be picked up (per user) from user environment.

  YAML SnippetXML Snippet

  jobs:
  - type: job
    namespace: diamond
    version: '4.0'
    name: preprocess
    id: ID0000001
    arguments: [-a, preprocess, -T, '60', -i, f.a, -o, f.b1, f.b2]
    uses:
    - {lfn: f.a, type: input}
    - {lfn: f.b2, type: output, stageOut: true, registerReplica: true}
    profiles:
      globus: {project: ${PROJECT}}
  

• Site Catalog

  In the site catalog, the site catalog entries are templated, where paths are resolved on the basis of values of environment variables. For example, below is a templated entry for a local site where $PWD is the working directory from where pegasus-plan is invoked.

  YAML SnippetXML Snippet

  sites:
  - name: local
    arch: x86_64
    os.type: linux
    directories:
    - type: sharedScratch
      path: ${PWD}/LOCAL/shared-scratch
      fileServers:
      - {url: 'file://${PWD}/LOCAL/shared-scratch', operation: all}
    - type: localStorage
      path: ${PWD}/LOCAL/shared-storage
      fileServers:
      - {url: 'file://${PWD}/LOCAL/shared-storage', operation: all}
  

• Replica Catalog

  The input file locations in the Replica Catalog can be resolved based on values of environment variables.

  YAML SnippetFile Snippet

  replicas:
    - lfn: input.txt
      pfns:
        - {site: local, pfn: 'http://${HOSTNAME}/pegasus/input/input.txt'}
  

  Note

  Variable expansion is only supported for YAML and File based Replica Catalog, not Regex or other file based formats.

• Transformation Catalog

  Similarly paths in the transformation catalog or profile values can be picked up from the environment i.e environment variables OS , ARCH and PROJECT are defined in user environment when launching pegasus-plan.

  YAML SnippetText Snippet

  transformations:
  - namespace: pegasus
    name: keg
    sites:
    - {name: isi,
       pfn: /path/to/keg,
       type: installed,
       arch:${ARCH},
       os: ${OS}}
    profiles:
      globus: {project: ${PROJECT}}