geneontology / noctua-landing-page

Noctua Search

An interface for the Search API

Endpoint

api/search

• Default sorting is date DESC recent models
• Default n models per page
• All the parameters are optional and by default it should bring recent n models with 'Date DESC'

Parameters

Parameter	Format	Comments
gps (optional)	list<gp>	A list of one or more gps in a model (AND operator)
goterms (optional)	list<goterm>	A list of one or more GO terms in a model (AND operator)
pmids (optional)	list<pmid>	A list of one or more pmids in a model (AND operator)
taxa (optional)	list<taxon>	A list of one or more taxon
Model Meta
title (optional)	string	Partial String (contains) so it works like the current landing page
states (optional)	list<state>	A list of one or more model states 'development, production, closed, review, delete' (OR operator)
contributors (optional)	list<contributor>	A list of one or more contributors in a model (AND operator)
groups (optional)	list<group>	A list of one or more groups(provided by) in a model (AND operator)
date (optional)	date	model date)
Pagination (optional, none or all)
page	int	Page number
offset	int	Page Offset
limit	int	Page Size

Return

total count matched models for progressive pagination when one needs second page

A list of

Parameter	Format	Comments
model id	iri	A model id
matched nodes	list<iri>	A list of one or more matched individual nodes
Model Meta
model title	string	A model title, first title annotation is fine if many
model state	string	A model's state
model date	string	A model modified date
model contributors	List<contributor>	A list of model's contributors
model groups	List<groups>	A list of model's groups (provided by)

Development server

Run npm start for a dev server. Navigate to http://localhost:4203/. The app will automatically reload if you change any of the source files.

noctua-landing-page's Issues

Model state not displaying on landing page for a particular model

From 2020-11-20 GO-CAM Jamboree

There is a mouse model that seems to have a model state value of development based on what is in the graph and form editors as well as the ttl file, but the model state doesn't display on the landing page table:

http://noctua.geneontology.org/workbench/noctua-form/?model_id=gomodel:586fc17a00000000

@tmushayahama Do you know why this might happen? Thx.

@hdrabkin

Task 1 - Welcome message for the NLP

Task requirement from Noctua Landing Page Project

• Create a welcome message
• Integrate and design the welcome message in the landing page (should be scrollable and not fixed)

Linked to #2

Add columns and icons for 'errors' and 'unsaved' model-level metadata

To allow curators to quickly assess some critical model-level metadata, add two additional columns to the table after the title on the landing page:

1. Errors (red exclamation point icon)

2. Unsaved (red disc icon)

Sort Lists, Groups, Contributors and Organisms

Sorting the list ascending alphabetically for the browse and lists.
Organisms sort by taxon name (asc)
Groups sort by group name (asc)
Contributors sort by name (asc)

tag: @vanaukenk

"exact term" is no longer default

Since the last update, it appears that searching on the exact term in no longer the default. One has to check the box to make it the default. I never had to do this before so I assume 'exact term' was the default.

Task 1 - Update the navigation bar look and feel and links

Task requirement from Noctua Landing Page Project

The navigation bar should have the same design as the one used on geneontology.org. Links to HTML pages and SASS from GO site:

• https://github.com/geneontology/geneontology.github.io/blob/master/_includes/topnav.html
• https://github.com/geneontology/geneontology.github.io/tree/master/_sass/custom

The GO logo should also be clickable and redirect to the main geneontology.org site.

The navigation bar should also contain two links:

• About Noctua
• Curation Manual

As well as a dropdown icon on the right for login/account preferences

Linked to #2

SARS-CoV2 is listed as a blank entry in the browse species list

Creating the ticket here since this is where the issue is visible, although the work may need to be done elsewhere.

The Browse species menu has a blank entry that, when clicked, shows three SARS-COV2-containing models.

We need to update the Browse species menu to list the proper species name for SARS-COV2.

Task 1 - global overview

This task relates to the layout and UI components of the Noctua Landing Page.

Notes:

• This repository will be based on the code of Noctua Search. As much as possible, this should be kept modular for sharing with Noctua Form and ART
• Unless (medium) or (low) is defined, the task is considered a high priority

Navigation bar / header

• share header with geneontology.org
• links & menu (left): GO website, About Noctua, Curation Manual
• login / account preference (right)

Footer

• same disclaimer as geneontology.org

Left content (BorderLayout.LEFT)

• welcome message (TBD by @vanaukenk)
• search/Browse panel (left) must be opened/unfolded by default
• remove filter button as essentially the same as search
• in Search panel, check with @vanaukenk for the appropriate orders of options (eg GO term, GP, PMID, etc)
• (medium priority) in search panel
  • add search by species
  • add search by specific & range date
  • fix term / gp autocomplete to show both label & id
• (medium priority) browse panel
  • use AGR species icon ? or look for SVG
  • add browse by species
  • add browse by date (specific & range)

Main content (BorderLayout.CENTER)

• show number of models; when search, show number of results / number of models
• GO-CAM table based on Noctua Search
  • add pagination (use MinervaAPI &count parameter)
  • remove "Apps" icon
  • table columns: Title, Date, Status, Contributors, Edit (form/graph), Export (GPAD/OWL)

Tooltips

• @vanaukenk revisit current tooltips and see what to change (eg Search -> Search GO-CAMs; @cmungall do we want Search models to be more generic ?)

add expand/collapse option to landing page to quickly scan annotations in models

From workbenches calls:

We'd like to add a new feature to the Noctua landing page to allow users to expand or collapse models so they can easily scan the individual annotations in models.

Thx.

Blank entries at the top of the list for Organism filter

Clicking on the Organism filter, there are eight blank entries at the top of the list:

Clicking on a blank entry brings up a fungal model for one of the species that Marc is curating.
We need to add these new species to the taxslim, I believe, as we had a similar issue when we first added SARS CoV2 models - see #30

@tmushayahama @balhoff @cmungall

Add Pathway Editor icon to the Open In menu on the Noctua landing page

Move the Visual Pathway Editor link out from under the three dot menu and include the link as an icon in the list of editorial interface icons.

@tmushayahama will create an icon based on results of google image search for 'icons pathway'

Consider adding an 'announcements' banner

It might be helpful users if we could add an 'announcements' banner to the Noctua landing page that could be used to announce, amongst other things, planned outages.

This would likely be an effective way of reaching active Noctua users.

Not a high priority issue for now.

not working filter on noctua new landing page search panel

I am using mac/firefox, here are some of the filters that didn't work when I tested:

filter by reference
fliter by date/date range
filter by title

Thanks,
Li

Browse by Species field is wrong size

@tmushayahama noticed the fields for each species are not large enough and cuts off top/bottom of text. Might be solved by increasing the width of that field to use up some of the blank real estate, would definitely be solved by increasing the height.

Add reference input helper popup

Just like on the Noctua Form, adding the reference popup to avoid input errors of to or not to include PMID

tag @vanaukenk

Save functionality under the Model Info section is not working

Reported by @suzialeksander

The Save functionality accessible from the Model Info section (to the right of a model, click on the three dots) of the landing page is not working.

The same functionality works fine on the Model Info section of the form and pathway editors.

@tmushayahama

Clear should clear all values

When I search using the Date Range and then try to reset the search by pressing 'Clear' at the bottom of the page, only the End Date cleared.

The Start Date retained the date I'd entered previously.

Add drop down menu to select number of models shown in results table

Like the current Noctua landing page, curators would like a drop down menu to select the number of models shown from a given search.

We should include a drop down of:
10
25
50
100

@sabrinatoro

Protein-containing complex (GO:0032991) and children no longer available in term search autocomplete

Trying to search on protein-containing complex (GO:0032991) or one of its children in the term search box, yields no terms from the ontology.

GO:0032991 and children are available for annotation in the graph editor and the CC only form.

New bug in mousing over form and graph icons

This is a new bug with the latest workbench updates.

On Noctua-dev, when I mouse over the form icon to the right of a model, the resulting text says 'Form Editor' (which is new text).
But now, if I move my mouse to the graph icon, the 'Form Editor' text doesn't go away and I can't click on the graph icon.
I have to move my mouse to another part of the landing page, come back, and can only get to the graph icon if I steer clear of the form icon, i.e. move my mouse from the far right side of the page.

This doesn't happen on production Noctua. I can move my mouse from the form to the graph icon and always get the right mouseover text and ability to click on the graph icon.

Figure out a way to limit what groups are listed on the landing page

The list of groups on the landing page reflects what is in the groups.yaml file, but that yaml file contains a number of groups that likely do not have annotations in GO nor will ever create GO-CAM models.

We need to make this list more user friendly by coming up with a subset that reflects GO content and Noctua use.

Putting this ticket here since this issue manifests on the landing page, but the work may require tickets in other trackers.

Enable searching on obsolete terms

It would be useful to be able to search for an obsolete term on the landing page. For example, if there is an obsolete term, I could ask ' show me all models/annotations that have an annotation to a term that has been obsoleted. '
This is important for the times that we fall behind the deadline time table for the spreadsheet reviews

Organisms on the autocomplete not displaying

They do display after a user clicks on the paw.

Getting all annotations to an obsolete term in a single search

As an add-on or perhaps concurrently with #98, the MGI curators would also like to be able to do a search that returns all annotations to obsolete terms. #98 allows for the search of individual terms, but curators would find it useful to be able to do the more global search to see if they have missed any clean-up. In those cases, they might not know which specific term on which to search.
ping @LiNiMGI

Task 1 - Update the footer look and feel and links

Task requirement from Noctua Landing Page Project

The footer should have the same design and links as the one used on geneontology.org. Links to HTML pages and SASS from GO site:

• https://github.com/geneontology/geneontology.github.io/blob/master/_includes/footer.html
• https://github.com/geneontology/geneontology.github.io/tree/master/_sass/custom

Linked to #2

Standardize Organism filter

Hello,

For all fields except for 'Organism', each box has 'filter by X'; while Organism has "Add organism filter" and is greyed out, see screenshot:

Is it possible to

• Change the text to 'Filter by organism'
• make the text the same color as other boxes

(Reported by Swiss-Prot curators:)

Thanks, Pascale

add ability to filter on model id from the landing page

A curator has asked for the ability to search on a model id from the landing page instead of having to paste it into the url. When doing QC reports, it is often easiest to find models by model id because that is what is listed in the GPAD properties. We should allow users to filter by model id on the landing page and it should become a user story for the ART.
ping @hdrabkin @vanaukenk