check and externalize explicit sparql queries #1284

[curibe]

related #1283, #1282, #785

Externalize explicit sparql queries

Converting the explicit queries (tables) first to externalized query format. For example, files who have the following queries:

somePanelDescriptionSparql = `
SELECT ...
...
`

This PR solves partially the issue #1284.

The following files still have explicit queries:

• 404_chemical.html
• author.html
• author-index-curation.html
• authors.html
• award_curation.html
• chemical-index-curation.html
• chemical-index.html
• lexeme_empty.html
• pathway_empty.html
• pathway.html
• property.html
• software_empty.html
• topic_curation.html
• use_empty.html
• use.html
• venue_curation.html
• venues.html
• work_cito.html
• work_empty.html
• works.html

Some annotations

• Files with empty will use the aspect as index but the name of html file will be the same for the moment. For example,
  use_empty.html have an aspect named use-index. The name of these html will be change in other PR
• Externalization for author.html, pathway.html and 404_chemical.html required the creation of new macros and custom JS functions for extracting queries to external .sparql files

[fnielsen]

Sorry, about the name pattern of the files not being clear. It should be aspect_panel-description, e.g., {% set aspect = "chemical-index" %}. This is confusingly used. So the file is chemical-index_statistics.sparql

[fnielsen]

venues are named fine!

[fnielsen]

Files called "empty" should be "index" instead, e.g., "work-index" and "pathway-index". Sorry again

[fnielsen]

award_curation -> award-curation

[curibe]

award_curation -> award-curation

@fnielsen In this case the html is called "award_curation.html". Do I still assign it in aspect as "award-curation"? no matter if the html file uses "_" or "-"?

[curibe]

Files called "empty" should be "index" instead, e.g., "work-index" and "pathway-index". Sorry again

@fnielsen Do you want to change the name only in the {%set aspect=....%} or also the html name?

[fnielsen]

award_curation -> award-curation

@fnielsen In this case the html is called "award_curation.html". Do I still assign it in aspect as "award-curation"? no matter if the html file uses "_" or "-"?

All HTML and sparql files should be called with a dash instead of an underscore

[curibe]

@fnielsen please, could you check this commit 4548191? A new macro was implemented together with JS functions in scholia.js

[curibe]

@fnielsen do you also require this caption here?

[fnielsen]

@fnielsen do you also require this caption here?

I am not sure what you mean?

[curibe]

@fnielsen do you also require this caption here?

I am not sure what you mean?

I refer to the caption shown in the red box. The function that shows the diagram does not a code implemented to display the
link, but another caption (below-left in the image : This diagram is showing... ):
https://scholia.toolforge.org/pathway/Q28031254

I put it to keep the format as the other externalizations. You can see the changes in this commit: a37c600
The caption was added here:

And It looks like this:

[fnielsen]

No a caption there is not necessary, I think. The rendering does not come from Wikimedia services, but from a thirdparty service, available at https://pathway-viewer.toolforge.org/?id=WP111 . I do not think they construct the visualization with SPARQL.

[fnielsen]

• cito_empty should be cito-index <aspect>_empty should be <aspect>-index #1554
• is venues iframe panels missing? http://127.0.0.1:8100/venues/Q1981225,Q5936947 venues iframe panels should be external #1553