noctua-landing-page's People
noctua-landing-page's Issues
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.
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.
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:
![image](https://private-user-images.githubusercontent.com/4782928/295140576-7b2996ef-a393-401f-9a2a-0670ca219484.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.4f0UUkmN6xWttyBn-H0ooxp2C8Lx_oR8ZMcvDmzfEfA)
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
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
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.
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.
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.
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
"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.
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
Add option or default to search over 'regulates' for 'Filter by Term' for models
The 'Filter by Term' search on the landing page does not search over the 'regulates' relation, which can result in models being missed.
So, searching with the term 'regulation of TOR signaling' retrieves 101 models, but 'TOR signaling' only retrieves 72 (and these are not all overlapping).
Would be useful to either have an option to 'include regulates' or just do this by default.
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
Organisms on the autocomplete not displaying
They do display after a user clicks on the paw.
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
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.
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.
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
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
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.
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 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
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
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'
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.
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
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:
-
Errors (red exclamation point icon)
-
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
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