geneontology / web-gocam Goto Github PK
View Code? Open in Web Editor NEWGO-CAM site as an Angular 2+ Application
Home Page: http://geneontology.org/go-cam
License: BSD 3-Clause "New" or "Revised" License
GO-CAM site as an Angular 2+ Application
Home Page: http://geneontology.org/go-cam
License: BSD 3-Clause "New" or "Revised" License
User Page GPs: the SPARQL UserMeta query which uses enabled_by also retrieve some GO-terms (should only retrieve GPs)
List of features and improvements discussed:
[EDIT]
Current state of development is updated.
[EDIT2]
Added features / suggestions / corrections from September 17 call
(*): multiple keywords can be either from the same column (e.g. finding the models with two biological processes: GO:0090090 GO:0021999) or from different columns (e.g. finding a model with a gene in a certain location: synapse RAB3)
The ability to browse development models, especially in the user page, is a general demand. It would help curators to access the models they are currently working on.
Several solutions exist:
Notes:
As the domain root, the current Drupal maintains a larger number of redirect, both to external resources, legacy page updates, and page renamings.; the webserver that hosts it likely many more.
While we will likely get rid of many of these, we will still have many cases where we'll want to redirect in various ways, some of them supporting this legacy.
This would be to implement a redirect system built into the new site's deployment, that reads from a structured file and redirects accordingly, editable by general GO users.
As a model, note the github.io system and https://github.com/jekyll/jekyll-redirect-from ; these could be directly used depending on the deployment method.
Two possibilities:
@cmungall to decide.
Wait for curators feedback and Integrate those models on the main page.
Title explains (most of) it all:
This View button should go to:
Not to the Noctua editorial interface.
@tmushayahama already has the code change in a branch. I can merge the change and deploy to AWS.
serverless, api gateway
currently on USC AWS account
Some curators have expressed the need to be able to search models having a specific GP or citing a specific PMID.
As suggested by @thomaspd, we should only show the most relevant (i.e., causal) GO-CAM models on the GO-CAM browser site.
I believe a fast way (perhaps we could call it a hack) to implement this is to just add the ?causlmf=2
parameter to the API call used to generate the cached gocam-models.json
file. The other three files shouldn't require any change as they're just lookup files for the main gocam-models.json
file.
The go-cam browser (https://geneontology.cloud/browse) currently just spin, with no display/browser created.
Looking at network traffic, everything seems to be fine: https://api.geneontology.cloud/models?last=12 returns just fine and the two S3 files seem to be there.
It actually looks like a code failure (at some level): ERROR TypeError: n.forEach is not a function
Wild guess: could be caused by cachingor related GO-CAM API issues (e.g. geneontology/api-gorest-2021#2 and geneontology/api-gorest#4) leading to mismatched objects leading to a null result that does not have an iterator.
I'd also guess the timing is related to the recent release. It may just need a kick (refresh).
Tagging @dustine32 and @tmushayahama and @sierra-moxon
Browse Page - Users: in the case of S.Toro, her name is sometime displayed twice, seems to be due to the fact the model was credited to 2 affiliations (using providedBy). The SPARL query used
The following announcement could impact both the GO-CAM website and the GO-CAM API as they are working with AWS SSL: https://aws.amazon.com/blogs/security/how-to-prepare-for-aws-move-to-its-own-certificate-authority/
At the moment, this doesn't seem to affect us, but will have to be monitored.
Number of GO-CAMs are not quite the same between the User Page and the Browse Page with User filter.
Note: with the current version of the blazegraph journal, respectively 48 and 53 GO-CAMs
This would be a fully fixed version of #21 (comment)
Some links at external locations point to the noctua curation system, creating load and outages for something that is not meant to be a public interface. An example (the only one?) is the pathway widget, which routes to a noctua view.
This would be closed when user all traffic associated with this repo is directed away from noctua (in conjunction with geneontology/api-gorest-2021#6).
Ability to download GOCAMs in SIF format:
Hello,
On the GO-CAM site https://geneontology.cloud/browse
gene products show up as IRIs/links - is this intended ?
I thought the gene name was shown
Thanks, Pascale
Remove GO-CAM download card from /go-cam site--the current one seems to contain items last updated in Dec 2020. As well, we are having a discussion about whether we are wanting to continue with the current SIF and JSON blob. After a discussion with @dustine32 , we believe it would be easier to re-implement (using existing or new code) than to fix. Adding new functionality with "fixed" downloads would be a different item. (Tagging @pgaudet and @cmungall ).
GOCAM site has a single entry point for documentation for each type of usage (research, curation, development):
The current Feedback component does not create GitHub tickets and there are discussions about using a 3rd party tool for handling feedbacks.
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