- slug: upload-metabolic-pathway
  name: Metabolic Pathway File
  requirements:
    expression-engine: jinja
    executor:
      docker:
        image: resolwe/base:ubuntu-17.10
    resources:
      network: true
  data_name: Metabolic Pathway
  version: 0.0.3
  type: data:metabolicpathway
  category: upload
  persistence: RAW
  scheduling_class: batch
  description: >
    Upload pathway json.
  input:
    - name: src
      label: Pathway file
      type: basic:file
      description: >
        JSON file. Supported extensions: '.json', '.json.gz'
      validate_regex: '(\.json)(\.gz)?$'
    - name: source
      label: Gene ID database
      type: basic:string
      allow_custom_choice: true
      choices:
        - label: BIGG
          value: BIGG
    - name: species
      label: Species
      type: basic:string
      choices:
        - label: Homo Sapiens
          value: Homo Sapiens
        - label: Mus musculus
          value: Mus musculus
  output:
    - name: pathway
      label: Pathway json
      type: basic:json
    - name: source
      label: Gene ID database
      type: basic:string
    - name: species
      label: Species
      type: basic:string
  run:
    runtime: polyglot
    language: bash
    program: |
      re-import {{ src.file_temp }} {{ src.file }} "json" "json" 0.5
      re-save pathway "${NAME}.json"
      re-save source {{ source }}
      re-save species {{ species }}

- slug: upload-metabolic-pathway
  name: Metabolic Pathway File
  requirements:
    expression-engine: jinja
    executor:
      docker:
        image: resolwe/base:ubuntu-17.10
    resources:
      network: true
  data_name: Metabolic Pathway
  version: 0.0.4
  type: data:metabolicpathway
  category: upload
  persistence: RAW
  scheduling_class: batch
  description: >
    Upload pathway json.
  input:
    - name: src
      label: Pathway file
      type: basic:file
      description: >
        JSON file. Supported extensions: '.json', '.json.gz'
      validate_regex: '(\.json)(\.gz)?$'
    - name: source
      label: Gene ID database
      type: basic:string
      allow_custom_choice: true
      choices:
        - label: BIGG
          value: BIGG
    - name: species
      label: Species
      type: basic:string
      choices:
        - label: Homo Sapiens
          value: Homo Sapiens
        - label: Mus musculus
          value: Mus musculus
  output:
    - name: pathway
      label: Pathway json
      type: basic:json
    - name: source
      label: Gene ID database
      type: basic:string
    - name: species
      label: Species
      type: basic:string
  run:
    runtime: polyglot
    language: bash
    program: |
      re-import {{ src.file_temp }} {{ src.file }} "json" "json" 0.5
      re-save pathway "${NAME}.json"
      re-save source {{ source }}
      re-save species {{ species }}

Replace Unicode character with ASCII equivalent
Replace Unicode character with ASCII equivalent
