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'env_local_scale' description contains double quotes #229

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turbomam opened this issue Jan 7, 2022 · 3 comments
Closed

'env_local_scale' description contains double quotes #229

turbomam opened this issue Jan 7, 2022 · 3 comments

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@turbomam
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turbomam commented Jan 7, 2022

As in

'"In this field, report the entity or entities which are in your
sample or specimenUs local vicinity and which you believe have significant causal
influences on your sample or specimen. Please use terms that are present in
ENVO and which are of smaller spatial grain than your entry for env_broad_scale.
Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel
[termID]|termLabel [termID]. Example: Annotating a pooled sample taken from
various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb
and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub
layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified
here: http://www.obofoundry.org/ontology/envo.html"'

Because double quotes were used in addition to >- ?

  env_local_scale:
    aliases:
      - local environmental context
    description: >-
       "In this field, report the entity or entities which are in your sample or specimenUs local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html"
    multivalued: false
    is_a: attribute
    range: controlled term value  ## syntax: {termLabel} {[termID]}
    pattern: ".* \\S+:\\S+"
    mappings:
      - mixs:env_local_scale
    in_subset:
      - environment
@turbomam turbomam changed the title env_local_scale description contains double quotes 'env_local_scale' description contains double quotes Jan 7, 2022
@turbomam
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in src/schema/mixs.yaml

if I fix this in that file, will it be overwritten by some Perl script @cmungall has spoken of?

@turbomam
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I tried replacing description: >-\s+" with description: " but pipenv run gen-yaml src/schema/nmdc.yaml said

File "", line 1150, column 5
expected , but found ''

File "", line 1152, column 81

because of double quotes in?

  votu_seq_comp_appr:
    aliases:
      - vOTU sequence comparison approach
    description: "Tool and thresholds used to compare sequences when computing ""species-level"" vOTUs"
    multivalued: false
    is_a: attribute
    range: text value  ## syntax: {software};{version};{parameters}
    mappings:
      - mixs:votu_seq_comp_appr
    in_subset:
      - sequencing

@wdduncan
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I manually removed double quotes surrounding descriptions.

turbomam added a commit that referenced this issue Oct 7, 2024
Backmerge 2024-07-16 (`nmdc-schema/main` -> `berkeley-schema-fy24/main`)
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