Go to Qiita Advent Calendar 2024 Top
LoginSignup
0
0

Delete article

Deleted articles cannot be recovered.

Draft of this article would be also deleted.

Are you sure you want to delete this article?

More than 5 years have passed since last update.

CWLAdvent Calendar 2017Day 18
@manabuishiirb(石井 学)

CWL User Guide 17: Metadata and Authorship をやってみた

Last updated at Posted at 2017-12-17

CWL User Guide 17: Metadata and Authorship

Metadata

今回は、メタデータと Authorshipについて書かれています

また、今回は、実行形式のファイルが２つあります。が、実行したというステップではないです。
最後の方に、schema-salad-tool での実行について書いてあったので、実行してみました。
２つとも、ながいエラーメッセージのようなものがみえていますが、valid であると出力されていました。

Key Points より

  • CWLでは、メタデータを与えることができます。
  • また、開発者は、正しい citation を与えるために、最低限の、 authorship に関する情報を提供することが望まれます。

この回にでてくる主なキーワード

  • $namespaces

CWLファイル1、metadata_example2.cwl

metadata_example2.cwl
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

label: An example tool demonstrating metadata.
doc: Note that this is an example and the metadata is not necessarily consistent.

inputs:
  aligned_sequences:
    type: File
    label: Aligned sequences in BAM format
    format: edam:format_2572
    inputBinding:
      position: 1

baseCommand: [ wc, -l ]

stdout: output.txt

outputs:
  report:
    type: stdout
    format: edam:format_1964
    label: A text file that contains a line count

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0002-6130-1021
    s:email: mailto:dyuen@oicr.on.ca
    s:name: Denis Yuen

s:contributor:
  - class: s:Person
    s:identifier: http://orcid.org/0000-0002-7681-6415
    s:email: mailto:briandoconnor@gmail.com
    s:name: Brian O'Connor

s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
s:dateCreated: "2016-12-13"
s:license: https://www.apache.org/licenses/LICENSE-2.0

$namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/

$schemas:
 - https://schema.org/docs/schema_org_rdfa.html
 - http://edamontology.org/EDAM_1.18.owl

schema-salad-tool 実行方法

自分は schema-salad-tool を以下のようにしていれました。

pip install schema_salad --user

その場合の実行方法はこうなります。
インストール方法によっては、第１引数のパスが違う可能性があります。

schema-salad-tool ~/.local/lib/python2.7/site-packages/schema_salad/tests/test_schema/CommonWorkflowLanguage.yml metadata_example2.cwl

schema-salad-tool 実行結果

$ schema-salad-tool ~/.local/lib/python2.7/site-packages/schema_salad/tests/test_schema/CommonWorkflowLanguage.yml metadata_example2.cwl
/home/vagrant/.local/bin/schema-salad-tool Current version: 2.6.20171116190026
No handlers could be found for logger "rdflib.term"
/home/vagrant/.local/lib/python2.7/site-packages/rdflib/plugins/parsers/structureddata.py:30: UserWarning: html5lib not found! RDFa and Microdata parsers will not be available.
  'parsers will not be available.')
Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: html5lib is not installed, cannot use RDFa and Microdata parsers.
metadata_example2.cwl:2:1: unrecognized extension field `https://schema.org/author`.  Did you include a $schemas section?
metadata_example2.cwl:2:1: unrecognized extension field `https://schema.org/contributor`.  Did you include a $schemas section?
metadata_example2.cwl:2:1: unrecognized extension field `https://schema.org/citation`.  Did you include a $schemas section?
metadata_example2.cwl:2:1: unrecognized extension field `https://schema.org/codeRepository`.  Did you include a $schemas section?
metadata_example2.cwl:2:1: unrecognized extension field `https://schema.org/dateCreated`.  Did you include a $schemas section?
metadata_example2.cwl:2:1: unrecognized extension field `https://schema.org/license`.  Did you include a $schemas section?
Document `metadata_example2.cwl` is valid

$ schema-salad-tool ~/.local/lib/python2.7/site-packages/schema_salad/tests/test_schema/CommonWorkflowLanguage.yml metadata_example3.cwl
/home/vagrant/.local/bin/schema-salad-tool Current version: 2.6.20171116190026
No handlers could be found for logger "rdflib.term"
/home/vagrant/.local/lib/python2.7/site-packages/rdflib/plugins/parsers/structureddata.py:30: UserWarning: html5lib not found! RDFa and Microdata parsers will not be available.
  'parsers will not be available.')
Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: html5lib is not installed, cannot use RDFa and Microdata parsers.
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/author`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/contributor`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/citation`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/codeRepository`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/dateCreated`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/license`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/keywords`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/programmingLanguage`.  Did you include a $schemas section?
Document `metadata_example3.cwl` is valid

CWLファイル2, metadata_example3.cwl

metadata_example3.cwl
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

label: An example tool demonstrating metadata.
doc: Note that this is an example and the metadata is not necessarily consistent.

hints:
  ResourceRequirement:
    coresMin: 4

inputs:
  aligned_sequences:
    type: File
    label: Aligned sequences in BAM format
    format: edam:format_2572
    inputBinding:
      position: 1

baseCommand: [ wc, -l ]

stdout: output.txt

outputs:
  report:
    type: stdout
    format: edam:format_1964
    label: A text file that contains a line count

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0002-6130-1021
    s:email: mailto:dyuen@oicr.on.ca
    s:name: Denis Yuen

s:contributor:
  - class: s:Person
    s:identifier: http://orcid.org/0000-0002-7681-6415
    s:email: mailto:briandoconnor@gmail.com
    s:name: Brian O'Connor

s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
s:dateCreated: "2016-12-13"
s:license: https://www.apache.org/licenses/LICENSE-2.0

s:keywords: edam:topic_0091 , edam:topic_0622
s:programmingLanguage: C

$namespaces:
 s: https://schema.org/
 edam: https://edamontology.org/

$schemas:
 - https://schema.org/docs/schema_org_rdfa.html
 - http://edamontology.org/EDAM_1.18.owl

schema-salad-tool の実行方法

schema-salad-tool ~/.local/lib/python2.7/site-packages/schema_salad/tests/test_schema/CommonWorkflowLanguage.yml metadata_example3.cwl

schema-salad-tool の実行結果

$ schema-salad-tool ~/.local/lib/python2.7/site-packages/schema_salad/tests/test_schema/CommonWorkflowLanguage.yml metadata_example3.cwl
/home/vagrant/.local/bin/schema-salad-tool Current version: 2.6.20171116190026
No handlers could be found for logger "rdflib.term"
/home/vagrant/.local/lib/python2.7/site-packages/rdflib/plugins/parsers/structureddata.py:30: UserWarning: html5lib not found! RDFa and Microdata parsers will not be available.
  'parsers will not be available.')
Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: html5lib is not installed, cannot use RDFa and Microdata parsers.
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/author`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/contributor`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/citation`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/codeRepository`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/dateCreated`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/license`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/keywords`.  Did you include a $schemas section?
metadata_example3.cwl:2:1: unrecognized extension field `https://schema.org/programmingLanguage`.  Did you include a $schemas section?
Document `metadata_example3.cwl` is valid

今回使ったファイル

cwl_user_guide_work/17-metadata at master · manabuishii/cwl_user_guide_work

0
0
0

Register as a new user and use Qiita more conveniently

  1. You get articles that match your needs
  2. You can efficiently read back useful information
  3. You can use dark theme
What you can do with signing up
Sign upLogin
0
0

Delete article

Deleted articles cannot be recovered.

Draft of this article would be also deleted.

Are you sure you want to delete this article?