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global replace OmicsProcessing with DataGeneration #1515

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aclum opened this issue Dec 12, 2023 · 6 comments · Fixed by microbiomedata/berkeley-schema-fy24#2
Closed

global replace OmicsProcessing with DataGeneration #1515

aclum opened this issue Dec 12, 2023 · 6 comments · Fixed by microbiomedata/berkeley-schema-fy24#2
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@aclum @SamuelPurvine @turbomam
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berkeley-fy24-refactor Label to describe issues created during the December 2023 hackathon for schema refactor

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@aclum
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aclum commented Dec 12, 2023

Replace all records of OmicsPrcessing with DataGeneration.
@aclum aclum added the berkeley-fy24-refactor Label to describe issues created during the December 2023 hackathon for schema refactor label Dec 12, 2023
@turbomam
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leave OmicsProcessing as an alias

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turbomam commented Dec 12, 2023 •
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  • cloned git@github.com:microbiomedata/berkeley-schema-fy24.git, which i s based on
  • opened in PyCharm
  • built poetry environment
  • currently running make squeaky-clean all test
    • want to confirm baseline functionality
    • next step: global find and replace, followed by another make squeaky-clean all test

@turbomam
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Omitting slots and slot_usages

  DataGeneration:
    aliases:
      - OmicsProcessing
      - assay
      - omics assay
      - sequencing project
      - experiment
    is_a: PlannedProcess
    in_subset:
      - sample subset
    description: >-
      The methods and processes used to generate omics data from a biosample or organism.
    alt_descriptions:
      embl.ena:
        An experiment contains information about a sequencing experiment including
        library and instrument details.
    broad_mappings:
      - OBI:0000070
      - ISA:Assay

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Now need to rename example files

turbomam added a commit to microbiomedata/berkeley-schema-fy24 that referenced this issue Dec 12, 2023
@turbomam
microbiomedata#1515 omicsproc -> datagen
c4f516b
@turbomam turbomam linked a pull request Dec 12, 2023 that will close this issue
Change Class:OmicsProcessing to Class:DataGeneration microbiomedata/berkeley-schema-fy24#2
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and omics_processing_set slot name -> data_generation_set

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turbomam commented Dec 12, 2023 •
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build succeeds now including examples, but we ahven't addressed typecodes yet

brynnz22 added a commit to microbiomedata/berkeley-schema-fy24 that referenced this issue Dec 12, 2023
@brynnz22
Merge pull request #2 from microbiomedata/1515-global-replace-omicspr…
7d5036f 
…ocessing-with-datageneration

microbiomedata#1515 omicsproc -> datagen
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@aclum aclum

@SamuelPurvine SamuelPurvine

@turbomam turbomam

Labels
berkeley-fy24-refactor Label to describe issues created during the December 2023 hackathon for schema refactor
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2023 Squad Sprint 25: December 4 - December 15, 2023
Status: Done
Refactoring Omics Processing Board
Status: Done
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Change Class:OmicsProcessing to Class:DataGeneration microbiomedata/berkeley-schema-fy24
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@aclum @SamuelPurvine @turbomam