phase-a-evaluate.yaml

# execute
#      mvn exec:exec -Dconfig=bioasq.phase-a-evaluate
# to test the pipeline

configuration:
  name: phase-a-evaluate
  author: ziy

persistence-provider:
  inherit: baseqa.persistence.local-sqlite-persistence-provider

collection-reader:
  inherit: baseqa.collection.json.json-collection-reader
  dataset: BIOASQ-QA
  file:
#    - input/one-question.json
#    - input/dryrun-a.json
#    - input/1b-1-a.json
#    - input/1b-2-a.json
#    - input/1b-3-a.json
#    - input/2b-1-a.json
#    - input/2b-2-a.json
#    - input/2b-3-a.json
#    - input/2b-4-a.json
#    - input/2b-5-a.json
#    - input/3b-1-a.json
#    - input/3b-2-a.json
#    - input/3b-3-a.json
#    - input/3b-4-a.json
    - input/3b-5-a.json
  decorators: |
    - inherit: bioasq.gs.bioasq-qa-gs-decorator
  persistence-provider: |
    inherit: baseqa.persistence.local-sqlite-persistence-provider

pipeline:
  - inherit: ecd.phase
    name: question-parse
    options: |
      - inherit: bioqa.question.parse.clearnlp-bioinformatics

  - inherit: ecd.phase
    name: question-concept-metamap
    options: |
      - inherit: bioqa.question.concept.metamap-cached

  - inherit: ecd.phase
    name: question-concept-tmtool
    options: |
      - inherit: bioqa.question.concept.tmtool-cached

  - inherit: ecd.phase
    name: question-concept-lingpipe-genia
    options: |
      - inherit: bioqa.question.concept.lingpipe-genia

  - inherit: ecd.phase
    name: concept-search-uts
    options: |
      - inherit: bioqa.evidence.concept.search-uts-cached

  - inherit: ecd.phase
    name: concept-merge
    options: |
      - inherit: baseqa.evidence.concept.merge

  - inherit: ecd.phase
    name: abstract-query-primary
    options: |
      - inherit: baseqa.abstract_query.token-concept

  # concept
  - inherit: ecd.phase
    name: concept-retrieval
    options: |
      - inherit: bioqa.concept.retrieval.lucene-bioconcept

  - inherit: ecd.phase
    name: concept-rerank
    options: |
      - inherit: bioqa.concept.rerank.liblinear-predict
      - inherit: base.noop

  # document
  - inherit: ecd.phase
    name: document-retrieval
    options: |
      - inherit: bioqa.document.retrieval.lucene-medline

  - inherit: ecd.phase
    name: document-rerank
    options: |
      - inherit: bioqa.document.rerank.liblinear-predict
      - inherit: base.noop

  # snippet
  - inherit: ecd.phase
    name: passage-retrieval
    options: |
      - inherit: bioasq.passage.retrieval.document-to-passage

  - inherit: ecd.phase
    name: passage-rerank
    options: |
      - inherit: bioqa.passage.rerank.liblinear-predict
      - inherit: base.noop

post-process:
  # concept evaluation
  - inherit: baseqa.eval.base
    calculator: |
      inherit: baseqa.eval.calculator.retrieval-eval-calculator
    evaluatee-provider: |
      inherit: baseqa.eval.evaluatee.concept-evaluatee-provider
    persistence-provider: |
      inherit: baseqa.eval.persistence.jdbc-eval-persistence-provider

  # document evaluation
  - inherit: baseqa.eval.base
    calculator: |
      inherit: baseqa.eval.calculator.retrieval-eval-calculator
    evaluatee-provider: |
      inherit: baseqa.eval.evaluatee.document-evaluatee-provider
    persistence-provider: |
      inherit: baseqa.eval.persistence.jdbc-eval-persistence-provider

  # trec passage evaluation
  - inherit: baseqa.eval.base
    calculator: |
      inherit: baseqa.eval.calculator.trec-passage-map-eval-calculator
    evaluatee-provider: |
      inherit: baseqa.eval.evaluatee.passage-evaluatee-provider
    persistence-provider: |
      inherit: baseqa.eval.persistence.jdbc-eval-persistence-provider

  # passage evaluation
  - inherit: baseqa.eval.base
    calculator: |
      inherit: baseqa.eval.calculator.passage-map-eval-calculator
    evaluatee-provider: |
      inherit: baseqa.eval.evaluatee.passage-evaluatee-provider
    persistence-provider: |
      inherit: baseqa.eval.persistence.jdbc-eval-persistence-provider

  # report
  - inherit: report.csv-report-generator
    builders: |
      - inherit: baseqa.report.accumulated-measurements-report-component