veupathdb / clinepiwebsite Goto Github PK

As mocked up here

If I want to find "SCORE S. mansoni" by typing into the filter in the Clinepi website's Studies menu, it won't work if I type SCORE S.

I have to type SCORE < because I happen to know there is an italic <i> tag in the study name.

Filtering should strip HTML first.

Pretty sure this is NOT a web-eda ticket - probably website related (don't know which repo). @jtlong3rd or @dmfalke can advise.

Cost is low though.

Right now we have 2 sets of qa sites, qa.clinepidb and qa.restricted.clinepidb. The only difference that I know of is that qa.clinepidb is restricted to show only studies where “isPublic” in the presenters is set to “true”. We don't really need the 2 different versions of the sites, but we do need a way to easily check which studies will be public with a release and which will remain on qa.

Brian suggested that we turn “isPublic” into a tag that we can use to filter on in the study summaries table as a way to check which studies will go out with a release. This would likely require service/client work to make sure all studies appear on the qa site, they are filterable based on the isPublic attribute, and that only those set to isPublic = true are accessible on the live site. However, if we make this change, it will allow us to get rid of qa.restricted.clinepidb.org and simplify things for the Systems and Outreach teams.

As part of this ticket, we could change the name of the annotation "isPublic" to "isReleased" to more clearly differentiate it from the data access level restrictions.

Will require edits to these files, I believe:

ClinEpiWebsite/Model/lib/conifer/roles/conifer/vars/ClinEpi/default.yml
ClinEpiWebsite/Model/lib/conifer/roles/conifer/vars/ClinEpi/production/default.yml

Depends on completion of client work detailed here: VEuPathDB/web-eda#822

To recreate:
Use the PRISM ICEMR Cohort and create a Line plot
X- axis: Age
Y-axis: Plasmodium asexual stages, by microscopy result
Function: Arithmetic mean (the same issue exists with median and geometric mean)

The plot should use the range of the means to set the Y-axis. However, it seems to be using the range of the raw Y variable data instead. This is problematic because it makes it look like a flat line with no data variation, whereas if you toggle on the log scale for the Y axis or change the default Y-axis range, you can see a strong relationship between age and parasite density.

https://qa.restricted.clinepidb.org/analysis/XhXiciQ

The new Site Search feature has now been implemented, with a new search box in the header. The "Find Studies" search box lower down on the ClinEpi home page should be removed.

To recreate. Try to download a file from SCORE Burundi (https://clinepidb.org/ce/app/workspace/analyses/DS_55fd455f5e/new/download) which has Controlled access. It brings up the data access popup. When I click on the "Submit data access" button, it brings up a screen that says "Loading" but never loads. Refreshing the page brings up the form.

This needs to be fixed so that the data access form loads without needing to refresh the page.

when the user scrolls down a page, for example the Study details tab, the tabs should always remain visible instead of scrolling out of view. We want the user to be able to "save their place" on the study details tab (for ex, a description of the study arms) so they can come back and refer to it as they are working on their analysis.

currently, the tabs scroll out of view so the user must navigate away from their position on the study details tab in order to navigate to the B&S tab

• the footer is too tall, please shrink the height of the footer

• it is not completely clear, in the footer, why all those icons are there. The relevance of the icons is to indicate that ClinEpiDB is part of a larger family of data resources. for a naive user, i am not sure they will understand. i wonder if the footer should make that more obvious.

Currently Microbiome user datasets are included in the ClinEpi studies header, but should be filtered out.

This ticket is to continue the work indicated in VEuPathDB/web-eda#769

Remaining task is to change placement of tagline and drop down menus according to mock-ups on slide 7 of this doc: https://docs.google.com/presentation/d/10DBhyRYbd3q6LEYZtiungGSVJ1nncir6llsTzLPyeH0/edit#slide=id.p

This can be done at the same time as the addition of the site search finder box

Discussed in 6/17/2022 EDA UX meeting

Terminology to differentiate official studies from DIY studies:

• DIY datasets will use the terminology: “User studies”
• ClinEpi studies will use the terminology: “Curated studies”

Changes needed:

On the “Study summaries” page:

• Page header should be: Study summaries
• Add a sub-header for User studies
• Add a sub-header for Curated studies

On the “My studies” summary page:

• Page header should be: My user studies

On the “My studies” page for a particular user dataset:

• Page header should be: My user studies: _My user study name_ (“My user study name” should be in italics, because every time text is editable (like “Analysis name”) it appears in italics)
• Change Use This Dataset in ClinEpiDB sub-header to Explore in ClinEpiDB (Explore in ClinEpiDB will be a link that takes you to an analysis page for this user study in the EDA)
• Remove hyperlinked study name under Use This Dataset in ClinEpiDB

On the dropdown menu:
Change Workspace > My studies to Workspace > My User Studies

We are currently not consistent in which release # and date we display for a study.

1. For studies with only 1 version, we display the release # and date correctly.
2. For studies with 2 versions, we display the second release # and date (e.g. Amazonia Brazil shows rel. 21 on 2022-Mar-03, which was the EDA release of the data and not rel.13 which was the original release)
3. For studies with 3 versions, we display the original release # and date (e.g. GEMS1 Case Control shows rel. 5 on 2018-Dec-13 rather than rel. 14 or 21)

First we need to decide what should be displayed (most recent version, original version, or a list of all versions?), then we need to implement that.

This is minor and can wait

see https://redmine.apidb.org/issues/43222

“Avg time to decision (days)” → amount of time between submission and decision to provide access or reject

decision was made to calculate the "avg time" statistic based on history logs (there is no need to take into account information from access requests made prior to the history log system being in place)

The data will come from the end_users table and the new history table.
Initially we thought of a new service endpoint but given that this information will be shown in existing pages:

• All Studies results table
• Study page
  Im hoping these will be new attributes/table in the study record xml (SQL)

More details:
avg_time_request_response_days:
1- is days enough granularity? YES (danica slack Jan 31 2021)
2- are we only considering transitions from request to another state? YES (danica slack Jan 31 2021)
----We may also want to consider time to 1st response as an additional stat

Originally reported in VEuPathDB/SiteSearchData#6 (comment)

In the tables for "Variables having this value" and "Study specific variable information", there is a column called "Study". Please rename this to "Study name" in both tables so that the terminology is used consistently

then the problem seems to be that the repo ClinepiWebsite is missing /images/ClinepiDB/favicon.ico under Site/webapp/
also in MicrobiomeWebsite
Api and Ortho are fine

im thinking we removed those directories by mistake in ClinepiWebsite and MicrobiomeWebsite..
maybe we want to have all in EbrcWebsite but we never got to do it..?

let's wait for dave what was his intention.

Nupur created a link for an unreleased study (https://clinepidb.org/ce/app/workspace/analyses/DS_0605f599e5) that the provider could put in a manuscript for when the study is released. However, the link not only works, but a guest can start an analysis from this. Ideally, a link like this should give a page not found error until the study is released

As mocked up here