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fix(JATS): Decoding tag table-wrap-foot for table #674

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merged 3 commits into from
Sep 9, 2020
Merged

fix(JATS): Decoding tag table-wrap-foot for table #674

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bd0ec61
fix(JATS): Decoding tag table-wrap-foot for table
AlexSisiucEndava Sep 7, 2020
ec9e64b
fix(JATS): Decode table description as an array of block content
nokome Sep 9, 2020
12b8ec7
test(PLOS): Update snapshots
nokome Sep 9, 2020
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5 changes: 5 additions & 0 deletions package-lock.json
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83 changes: 83 additions & 0 deletions src/codecs/jats/__file_snapshots__/elife-30274-v1.yaml
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Expand Up @@ -3113,6 +3113,37 @@ content:
depth: 3
content:
- Confirmatory statistical tests.
description:
- type: Paragraph
content:
- >-
These confirmatory statistical tests relate to the data presented
in
- type: Link
relation: fig
target: '#fig2'
content:
- Figure 2
- >-
. Wilcoxon signed-rank test, which treat the data as paired, were
conducted for the original study (
- type: Cite
target: bib17
content:
- 'Lin et al., 2012'
- ') and this replication attempt (RP:CB). Uncorrected '
- type: Emphasis
content:
- p
- ' values are reported with an '
- type: Emphasis
content:
- a priori
- ' significance threshold of. 0167. Sample sizes reported are based on the sample size used in the tests. Additional details for this experiment can be found at '
- type: Link
target: 'https://osf.io/fn2y4/.'
content:
- 'https://osf.io/fn2y4/.'
label: Table 1.
rows:
- type: TableRow
Expand Down Expand Up @@ -3493,6 +3524,31 @@ content:
depth: 3
content:
- Exploratory statistical tests.
description:
- type: Paragraph
content:
- 'These exploratory statistical tests relate to the data presented in '
- type: Link
relation: fig
target: '#fig2'
content:
- Figure 2
- >-
. Wilcoxon rank sum tests, which treat the data as unpaired, were
conducted for the original study (
- type: Cite
target: bib17
content:
- 'Lin et al., 2012'
- ') and this replication attempt (RP:CB). Uncorrected '
- type: Emphasis
content:
- p
- ' values are reported. Sample sizes reported are based on treating genes as unpaired between conditions. Additional details for this experiment can be found at '
- type: Link
target: 'https://osf.io/fn2y4/.'
content:
- 'https://osf.io/fn2y4/.'
label: Table 2.
rows:
- type: TableRow
Expand Down Expand Up @@ -3908,6 +3964,33 @@ content:
depth: 3
content:
- Exploratory statistical tests.
description:
- type: Paragraph
content:
- 'These exploratory statistical tests relate to the data presented in '
- type: Link
relation: fig
target: '#fig2'
content:
- Figure 2
- . Wilcoxon rank sum tests were conducted for the original study (
- type: Cite
target: bib17
content:
- 'Lin et al., 2012'
- >-
) and this replication attempt (RP:CB) on the difference in
expression of active genes during c-Myc induction (e.g. from 0 hr to
24 hr) compared to the difference in expression of silent genes over
that same period (e.g. from 0 hr to 24 hr). Uncorrected
- type: Emphasis
content:
- p
- ' values are reported. Sample sizes reported are based on number of active and silent genes used in the tests. Additional details for this experiment can be found at '
- type: Link
target: 'https://osf.io/fn2y4/.'
content:
- 'https://osf.io/fn2y4/.'
label: Table 3.
rows:
- type: TableRow
Expand Down
64 changes: 64 additions & 0 deletions src/codecs/jats/__file_snapshots__/elife-46472-v3.yaml
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Expand Up @@ -5021,6 +5021,70 @@ content:
content:
- Oprm1
- ' genotype combinations for the BXD strains.'
description:
- type: Paragraph
content:
- >-
Abbreviations: BXD, C57BL/6J (B6) x DBA2/J (D2); MA,
methamphetamine;
- type: Emphasis
content:
- Oprm1
- ', mu-opioid receptor gene; '
- type: Emphasis
content:
- Oprm1
- type: Superscript
content:
- B6/B6
- ', homozygous for B6 '
- type: Emphasis
content:
- Oprm1
- ' allele; '
- type: Emphasis
content:
- Oprm1
- type: Superscript
content:
- D2/D2
- ', homozygous for D2 '
- type: Emphasis
content:
- Oprm1
- ' allele; '
- type: Emphasis
content:
- Taar1
- ', trace-amine associated receptor 1 gene; '
- type: Emphasis
content:
- Taar1
- type: Superscript
content:
- +/+
- ', homozygous for reference '
- type: Emphasis
content:
- Taar1
- type: Superscript
content:
- +
- ' allele; '
- type: Emphasis
content:
- Taar1
- type: Superscript
content:
- m1J/m1J
- ', homozygous for mutant '
- type: Emphasis
content:
- Taar1
- type: Superscript
content:
- m1J
- ' allele.'
label: Table 1.
rows:
- type: TableRow
Expand Down
21 changes: 21 additions & 0 deletions src/codecs/jats/__file_snapshots__/f1000-7-1655-v1.yaml
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Expand Up @@ -819,6 +819,27 @@ content:
depth: 3
content:
- Article-type attributes.
description:
- type: Paragraph
content:
- type: Strong
content:
- Note
- >-
: aggregated-review-documents is not currently in the Crossref
schema; that schema uses the term aggregate. Crossref has two
further attributes to describe the type of content:

- type: Strong
content:
- community-comment
- |2-
and

- type: Strong
content:
- manuscript.
- ' The XML sub-group discussed these terms and decided to exclude them as community-comment presumably refers to post-publication comments via systems like Hypothesis and so: a) are not guaranteed to be “peer” comments and are excluded from the criteria of this paper and b) it is unlikely that publishers in the near term would pull that content back into the source JATS XML, post publication. Crossref schema also allows for a stage, pre-publication or post-publication. This is therefore also felt outside of this remit.'
label: 'Table 1. '
rows:
- type: TableRow
Expand Down
108 changes: 108 additions & 0 deletions src/codecs/jats/__file_snapshots__/f1000-8-1394-v1.yaml
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Expand Up @@ -1147,6 +1147,37 @@ content:
- >-
Cannabidiol (CBD) stability experiments under various storage
conditions.
description:
- type: Paragraph
content:
- type: Superscript
content:
- '1'
- |2-
Average of LC-MS/MS and UPLC-QTOF measurements (n=2) (for raw results see dataset

- type: Superscript
content:
- type: Cite
target: ref-13
content:
- '13'
- >-
, table sheet 1). THC formation calculated as % in relation to
original CBD content.
- type: Paragraph
content:
- |-
Abbreviations: CBD: cannabidiol; THC: Δ

- type: Superscript
content:
- '9'
- >-
-tetrahydrocannabinol; UVA: ultraviolet A; LC-MS/MS: liquid
chromatography/tandem mass spectrometry; UPLC-QTOF: ultra-high
pressure liquid chromatography/quadrupole time-of-flight mass
spectrometry
label: 'Table 1. '
rows:
- type: TableRow
Expand Down Expand Up @@ -1787,6 +1818,83 @@ content:
- >-
Results of THC analysis in commercial products based on hemp
extracts from the German market (2018–2019).
description:
- type: Paragraph
content:
- type: Superscript
content:
- '1'
- |2-
Average of 1–6 replicates measured with LC-MS/MS reported (for raw results see dataset

- type: Superscript
content:
- type: Cite
target: ref-13
content:
- '13'
- ', table sheet 2).'
- type: Paragraph
content:
- type: Superscript
content:
- '2'
- ' Not analyzed or outside calibration.'
- type: Paragraph
content:
- type: Superscript
content:
- '3'
- ' No labelling provided by manufacturer.'
- type: Paragraph
content:
- type: Superscript
content:
- '4'
- ' THC (mg/day) calculated on the basis of 1 portion according to the manufacturer’s labelling. The LOAEL may be exceeded with a probable intake of 2 portions/day.'
- type: Paragraph
content:
- type: Superscript
content:
- '5'
- |2-
The German guideline value for THC content in food products is 150 µg/kg

- type: Superscript
content:
- type: Cite
target: ref-14
content:
- '14'
- .
- type: Paragraph
content:
- |-
Abbreviations: CBD: cannabidiol; THC: Δ

- type: Superscript
content:
- '9'
- >-
-tetrahydrocannabinol; ARfD: acute reference dose (ARfD) of 1 μg THC
per kg body weight

- type: Superscript
content:
- type: Cite
target: ref-15
content:
- '15'
- |-
; LOAEL: lowest observed adverse effect level of 2.5 mg THC per day

- type: Superscript
content:
- type: Cite
target: ref-15
content:
- '15'
- '; LC-MS/MS: liquid chromatographic/tandem mass spectrometric'
label: 'Table 2. '
rows:
- type: TableRow
Expand Down
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