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Improve handing of author notes by adding support for corresp string #1081

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merged 28 commits into from
Sep 5, 2024
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939bdf0
add test for authorNotes meta field to include corresp and types
will-byrne Aug 20, 2024
eb07fbb
Add type 'fn' to authorNotes in decodeMetaFront
soggy-mushroom Aug 20, 2024
62a7dbe
update snapshots for authorNotes type test changes
will-byrne Aug 20, 2024
ed53a2f
Adjust snapshots and test case to include type 'fn' in authorNotes
soggy-mushroom Aug 20, 2024
d944835
add coresp authorNote and update tests and snapshots
will-byrne Aug 20, 2024
07090aa
add failing test for corresp entry in author meta
will-byrne Aug 22, 2024
936627b
Remove the emails array functionality
soggy-mushroom Aug 28, 2024
cb0b4a6
Adjust the first 4 snapshots of meca to json
soggy-mushroom Aug 28, 2024
99a3cef
Adjust the remaining test fixtures for MECA to JSON test
soggy-mushroom Aug 28, 2024
c383a6f
feat: remove email addresses from JATS codec file snapshots
nlisgo Aug 28, 2024
2bede67
feat: remove email addresses from JATS snapshots
nlisgo Aug 28, 2024
b533ae5
feat: remove email from elife-46472-v3 file in jats codec
nlisgo Aug 28, 2024
73f30f3
feat: remove email detail from elife-46793-v1.yaml file
nlisgo Aug 28, 2024
47bb482
feat: remove email from elife-52882-v2.yaml file snapshot in jats codec
nlisgo Aug 28, 2024
6638694
feat: Remove email attributes from JATS codec snapshots
nlisgo Aug 28, 2024
c136d46
Remove email addresses from more yaml fixtures
soggy-mushroom Aug 28, 2024
f3b9ca4
feat: remove emails from f1000 snapshots in JATS codec
nlisgo Aug 28, 2024
0deeb35
feat: change corresp label from '+' to '*' in jats tests
nlisgo Aug 28, 2024
b5dc4d3
feat: enhance decoding of meta front in JATS codec
nlisgo Aug 28, 2024
4904188
feat: Add 'corresp' reference type to JATS codec
nlisgo Aug 28, 2024
dc93fed
feat(jats codec): add corresp and fn types to meta notes
nlisgo Aug 28, 2024
2b158b7
feat: Update meta notes format in several yaml files
nlisgo Aug 28, 2024
45eb531
feat: adjust indentation in decodeMetaFront function in jats codec
nlisgo Aug 28, 2024
8d6428a
Add back email parsing fuctionality apart from corresp bit and adjust…
soggy-mushroom Aug 29, 2024
b920173
Adjust the remaining jats snapshots to include emails
soggy-mushroom Aug 29, 2024
f7f8429
cs
nlisgo Aug 29, 2024
17e29f2
feat(jats): remove unused import 'fastest-levenshtein' from jats/inde…
nlisgo Aug 29, 2024
5466ee1
chore(release): bump version for release
nlisgo Sep 5, 2024
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2 changes: 1 addition & 1 deletion package.json
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "@stencila/encoda",
"version": "1.0.4",
"version": "1.0.5",
"description": "Codecs for executable document formats",
"files": [
"install.js",
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -30,15 +30,21 @@
"authors": [
{
"type": "Person",
"emails": [
"[email protected]"
],
"familyNames": [
"Mallard"
],
"givenNames": [
"François"
]
],
"meta": {
"notes": [
{
"type": "corresp",
"label": "*",
"rid": "cor1"
}
]
}
},
{
"type": "Person",
Expand All @@ -51,15 +57,21 @@
},
{
"type": "Person",
"emails": [
"[email protected]"
],
"familyNames": [
"Teotónio"
],
"givenNames": [
"Henrique"
]
],
"meta": {
"notes": [
{
"type": "corresp",
"label": "*",
"rid": "cor1"
}
]
}
}
],
"dateAccepted": {
Expand Down Expand Up @@ -4882,7 +4894,16 @@
}
],
"title": "Selection and the direction of phenotypic evolution",
"meta": {},
"meta": {
"authorNotes": [
{
"type": "corresp",
"id": "cor1",
"label": "*",
"text": " Corresponding authors: [email protected]; [email protected]."
}
]
},
"content": [
{
"type": "Paragraph",
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -122,9 +122,6 @@
"name": "Department of Plant Biology, University of California, One Shields Avenue, Davis, CA 95616"
}
],
"emails": [
"[email protected]"
],
"familyNames": [
"Harmer"
],
Expand All @@ -138,7 +135,16 @@
"propertyID": "https://registry.identifiers.org/registry/orcid",
"value": "http://orcid.org/0000-0001-6813-6682"
}
]
],
"meta": {
"notes": [
{
"type": "corresp",
"label": "*",
"rid": "cor1"
}
]
}
}
],
"dateAccepted": {
Expand Down Expand Up @@ -4246,7 +4252,16 @@
}
],
"title": "The circadian clock controls temporal and spatial patterns of floral development in sunflower",
"meta": {},
"meta": {
"authorNotes": [
{
"type": "corresp",
"id": "cor1",
"label": "*",
"text": "Correspondence to [email protected]"
}
]
},
"content": [
{
"type": "Heading",
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,9 @@
"meta": {
"notes": [
{
"rid": "n1",
"label": "*"
"type": "fn",
"label": "*",
"rid": "n1"
}
]
}
Expand All @@ -76,8 +77,9 @@
"meta": {
"notes": [
{
"rid": "n1",
"label": "*"
"type": "fn",
"label": "*",
"rid": "n1"
}
]
}
Expand Down Expand Up @@ -215,15 +217,21 @@
"name": "State Key Laboratory of Pharmaceutical Biotechnology, Department of Vascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008"
}
],
"emails": [
"[email protected]"
],
"familyNames": [
"Qiao"
],
"givenNames": [
"Tong"
]
],
"meta": {
"notes": [
{
"type": "corresp",
"label": "#",
"rid": "cor1"
}
]
}
},
{
"type": "Person",
Expand All @@ -245,9 +253,6 @@
"name": "Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210093"
}
],
"emails": [
"[email protected]"
],
"familyNames": [
"Li"
],
Expand All @@ -260,7 +265,16 @@
"propertyID": "https://registry.identifiers.org/registry/orcid",
"value": "http://orcid.org/0000-0001-9738-049X"
}
]
],
"meta": {
"notes": [
{
"type": "corresp",
"label": "#",
"rid": "cor1"
}
]
}
}
],
"dateAccepted": {
Expand Down Expand Up @@ -3945,9 +3959,16 @@
"meta": {
"authorNotes": [
{
"type": "fn",
"id": "n1",
"label": "*",
"text": "Tianze Xu and Jing Cai contributed equally to this work"
},
{
"type": "corresp",
"id": "cor1",
"label": "#",
"text": "Corresponding authors: Dr. Kuanyu Li, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210093, P. R. China. Email: [email protected]; Dr. Tong Qiao. Email: [email protected]"
}
]
},
Expand Down
39 changes: 30 additions & 9 deletions src/codecs/jats/__file_snapshots__/87253.json
Original file line number Diff line number Diff line change
Expand Up @@ -36,15 +36,21 @@
"name": "Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK"
}
],
"emails": [
"[email protected]"
],
"familyNames": [
"Cacioppo"
],
"givenNames": [
"Roberta"
]
],
"meta": {
"notes": [
{
"type": "corresp",
"label": "*",
"rid": "cor1"
}
]
}
},
{
"type": "Person",
Expand Down Expand Up @@ -112,9 +118,6 @@
"name": "Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK"
}
],
"emails": [
"[email protected]"
],
"familyNames": [
"Lindon"
],
Expand All @@ -127,7 +130,16 @@
"propertyID": "https://registry.identifiers.org/registry/orcid",
"value": "http://orcid.org/0000-0003-3554-2574"
}
]
],
"meta": {
"notes": [
{
"type": "corresp",
"label": "*",
"rid": "cor1"
}
]
}
}
],
"dateAccepted": {
Expand Down Expand Up @@ -7159,7 +7171,16 @@
}
],
"title": "Differential translation of mRNA isoforms underlies oncogenic activation of cell cycle kinase Aurora A",
"meta": {},
"meta": {
"authorNotes": [
{
"type": "corresp",
"id": "cor1",
"label": "*",
"text": "To whom correspondence should be addressed. Email: Roberta Cacioppo [email protected] or Catherine Lindon [email protected]."
}
]
},
"content": [
{
"type": "Heading",
Expand Down
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