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Add Author objects #103

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@dosumis dosumis commented Mar 12, 2024

Author objects - draft #102

Author objects - draft #102
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Validation Passes.

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dosumis commented Apr 4, 2024

Before we merge this, we need a strategy for compatibility with CAP author fields.

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Validation Passes.

@dosumis dosumis changed the title Update general_schema.json Add Author objects May 22, 2024
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dosumis commented May 22, 2024

TBD - do we still need a separate string field for author?

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dosumis commented May 22, 2024

Discussed in DOS group call. Still not clear how to proceed if we want bidirectional conversion with CAP.
This would be fixed if CAP changed their AnnData specification to support an author table (dataframe) in uns, where each row has various author details - ditching the currently separate fields for this.

@evanbiederstedt - please comment.

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CC @rm1113

I think this can be closed and disregarded CC @ubyndr

In the end, we decided to not use additional fields for list of authors. So the old logic is fine.

@ubyndr ubyndr closed this May 23, 2024
@dosumis dosumis reopened this Jun 7, 2024
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dosumis commented Jun 7, 2024

Reopening based on discussion with @evanbiederstedt

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github-actions bot commented Jun 7, 2024

Validation Passes.

- Removed author fields from primary properties.  
- Author_list now takes a list of objects with first author first in list
- minor tweaks to author object property field names and text
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github-actions bot commented Jun 7, 2024

Validation Passes.

Also reverted author object requirements in CAP as Evan doesn't think we can enforce for all authors.  Requirement for email and orcid for first author will move to CAP business logic
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github-actions bot commented Jun 7, 2024

Validation Passes.

@dosumis dosumis requested review from ubyndr and JABelfiore June 7, 2024 20:01
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dosumis commented Jun 7, 2024

Hi @JABelfiore & @ubyndr - did some work on this with @evanbiederstedt - can you please review. Ta

@@ -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>
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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.

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We should write keys with empty values @rm1113

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Validation Passes.

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dosumis commented Jun 23, 2024

@hkir-dev @ubyndr I'm happy with this, but there are backwards compatibility issues, so we will need a plan for updating existing taxonomies before releasing.

@hkir-dev - can you plan for this and estimate the work involved?

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hkir-dev commented Jun 26, 2024

We need to update:

  • cas-tools data classes
  • update and test anndata2cas, abc2cas, spreadsheet2cas, flatten and merge (1 man day)
  • update the TDT data ingestion and export (0.5 man day)
  • update 10 taxonomy repositories (0.5 man day)

Additionally we will need a new TDT function that will harmonise existing manual taxonomy curations to this kind of data structure changes. Since we don't have any manual curations in the taxonomies yet, we are recreating TDT tables from scratch now.

Comment on lines -204 to -207
"author_name": {
"description": "Primary author's name. This MUST be a string in the format `[FIRST NAME] [LAST NAME]`",
"type": "string"
},
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Since this has been removed, don't we need to remove it from;

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

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5 participants