Skip to content

Add Author objects #103

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 7 commits into
base: main
Choose a base branch
from
Open

Add Author objects #103

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
d081b7e
Update general_schema.json
dosumis Mar 12, 2024
5f24686
Update general_schema.json
dosumis May 22, 2024
202dcad
Update general_schema.json
dosumis May 22, 2024
7f34682
Merge branch 'main' into author-object
dosumis Jun 7, 2024
35b5473
Update general_schema.json
dosumis Jun 7, 2024
327d316
Aligned CAP_anndata_spec
dosumis Jun 7, 2024
f435746
change source and author_contact fields
rm1113 Jun 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 16 additions & 16 deletions docs/cap_anndata_schema.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1240,22 +1240,22 @@ Key-value pair in the `uns` dictionary
</tr>
</tbody></table>

## authors_list
## author_list

Key-value pair in the `uns` dictionary

<table><tbody>
<tr>
<td><b>key</b></td>
<td><code>authors_list</code></td>
<td><code>author_list</code></td>
</tr>
<tr>
<td><b>type</b></td>
<td>string</td>
<td>List of dictionaries</td>
</tr>
<tr>
<td><b>value</b></td>
<td>This field stores a list of CAP users who are included in the CAP project as collaborators, regardless of their specific role (Viewer, Editor, or Owner).</td>
<td>This field stores a list of CAP users who are included in the CAP project as collaborators. The first author in this list is the primary author on CAP.`</td>
</tr>
<td><b>source</b></td>
<td>software</td>
Expand All @@ -1266,13 +1266,13 @@ Key-value pair in the `uns` dictionary
</tr>
<tr>
<td><b>example</b></td>
<td><code>'['John Smith', 'Cody Miller', 'Sarah Jones']'</code></td>
<td><code>'[{'author_name':'John Smith', 'email':'[email protected]', 'orcid' :'ORCID:0000-0002-3843-3472'}]'</code></td>
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It is not clear what to do in case of empty fields. Should we still write keys with empty values like 'email': None or we can just skip it.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

We should write keys with empty values @rm1113

</tr>
</tbody></table>

## author_name
### author_name

Key-value pair in the `uns` dictionary
Key-value pair in the `author_list` item dictionary

<table><tbody>
<tr>
Expand All @@ -1289,7 +1289,7 @@ Key-value pair in the `uns` dictionary
</tr>
<tr>
<td><b>source</b></td>
<td>file or UI</td>
<td>software</td>
</tr>
<tr>
<td><b>required for publication on CAP</b></td>
Expand All @@ -1302,14 +1302,14 @@ Key-value pair in the `uns` dictionary
</tbody></table>


## author_contact
### email

Key-value pair in the `uns` dictionary
Key-value pair in the `author_list` item dictionary

<table><tbody>
<tr>
<td><b>key</b></td>
<td><code>author_contact</code></td>
<td><code>email</code></td>
</tr>
<tr>
<td><b>type</b></td>
Expand All @@ -1321,7 +1321,7 @@ Key-value pair in the `uns` dictionary
</tr>
<tr>
<td><b>source</b></td>
<td>file or UI</td>
<td>software</td>
</tr>
<tr>
<td><b>required for publication on CAP</b></td>
Expand All @@ -1333,14 +1333,14 @@ Key-value pair in the `uns` dictionary
</tr>
</tbody></table>

## author_orcid
### orcid

Key-value pair in the `uns` dictionary
Key-value pair in the `author_list` item dictionary

<table><tbody>
<tr>
<td><b>key</b></td>
<td><code>author_orcid</code></td>
<td><code>orcid</code></td>
</tr>
<tr>
<td><b>type</b></td>
Expand All @@ -1352,7 +1352,7 @@ Key-value pair in the `uns` dictionary
</tr>
<tr>
<td><b>source</b></td>
<td>file or UI</td>
<td>software</td>
</tr>
<tr>
<td><b>required for publication on CAP</b></td>
Expand Down
41 changes: 26 additions & 15 deletions general_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,29 @@
"description": "A general, open-standard schema for cell annotations which records connections, types, provenance and evidence.\nThis is designed not to tie-in to a single project (i.e. no tool-specific fields in core schema),and allows for extensions to support ad hoc user fields, new formal schema extensions, and project/tool specific metadata.",
"type": "object",
"definitions": {
"Author": {
"required": [
"author_name"
],
"properties": {
"author_name": {
"description": "Author name. This MUST be a string in the format `[FIRST NAME] [LAST NAME]`",
"type": "string"
},
"orcid": {
"description": "Author's ORCID. This MUST be a valid ORCID for the author in the form ORCID:0000-0002-7073-9172",
"type": "string"
},
"github_username": {
"description": "Authors GitHub handle.",
"type": "string"
},
"email": {
"description": "Author's contact email address.",
"type": "string"
}
}
},
"Review": {
"required": ["datestamp", "verdict"],
"additionalProperties": false,
Expand Down Expand Up @@ -198,21 +221,9 @@
"type": "string"
},
"author_list": {
"description": "This field stores a list of users who are included in the project as collaborators, regardless of their specific role. An example list; '['John Smith', 'Cody Miller', 'Sarah Jones']'",
"type": "string"
},
"author_name": {
"description": "Primary author's name. This MUST be a string in the format `[FIRST NAME] [LAST NAME]`",
"type": "string"
},
Comment on lines -204 to -207
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Since this has been removed, don't we need to remove it from;

  "required": [
    "author_name",
    "annotations",
    "labelsets"
  ],

"author_contact": {
"description": "Primary author's contact. This MUST be a valid email address of the author",
"type": "string",
"format": "email"
},
"orcid": {
"description": "Primary author's orcid. This MUST be a valid ORCID for the author",
"type": "string"
"description": "This field stores a list of authors, The first author must be the primary author of the dataset on publication.",
"type": "array",
"$ref": "#/definitions/Author"
},
"labelsets": {
"type": "array",
Expand Down
Loading