search

microbiomedata / nmdc-server

Data portal client and server for NMDC.
https://data.microbiomedata.org
Other
9 stars 0 forks source link

Typos on the NMDC Data Portal - Project landing pages #648

Closed mslarae13 closed 1 year ago

mslarae13 commented 2 years ago

The SPRUCE study landing page has a typo in the study description “Focus Area of ORNL”s Climate” … ORNL”s should be ORNL’s

Also, do we have the ability to subscript the 2 in CO2 ?

mslarae13 commented 2 years ago

Comment from @dwinston via slack " I see that there is (correctly) a single-quote in the nmdc-runtime metadata store (i.e. mongodb): https://api.dev.microbiomedata.org/studies?filter=description.search%3ASPRUCE . I also see that the study name in the metadata store is "Peatland microbial communities from Minnesota, USA, analyzing carbon cycling and trace gas fluxes", whereas the header line on https://data.microbiomedata.org/details/study/gold:Gs0110138 begins "Fungal, bacterial, and archaeal communities mediating...". So, it seems that code from the nmdc-server repo (github.com/microbiomedata/nmdc-server/) is doing some custom overriding/transformation of values that is incorrect in this case (for the study description). To subscript the 2 in CO2, that would be a mater of the nmdc-server repo in how it renders text. It could be revised to detect chemical formulae, or perhaps we could include tagging in the text, e.g. "...CO2..", that the portal renderer could interpret consistently. Either way, the nmdc-server code would need to render it properly. "

subdavis commented 2 years ago

single quote vs double quote.

Probably a string escaping issue somewhere. That's probably something I can fix.

name vs title

The portal uses the title instead of the name field if it's available, which is what @dwinston said I should do in June 2021. If the title is wrong, it should probably be corrected in mongo?

From Donny: "5 of the 8 documents in the study_set collection have title fields in addition to name fields. The name field is being displayed for all 8 studies currently. If a study has a title field set, that should be displayed instead of the value of the name field."

subscript CO2

Can we simply use unicode subscript? Anything working with strings should support it. CO₂

dwinston commented 2 years ago

The portal uses the title instead of the name field if it's available

Ah, right.

mslarae13 commented 2 years ago

@dwinston & @mcovalt Checking in on this. Looks like it was fixed. https://data.microbiomedata.org/details/study/gold:Gs0110138

mslarae13 commented 2 years ago

Typos were fixed... but the study description disappearing still needs fixed. Should be "This study is part of the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, which is the primary component of the Terrestrial Ecosystem Science Focus Area of ORNL's Climate Change Program, focused on terrestrial ecosystems and the mechanisms that underlie their responses to climatic change. This project seeks to assess the response of northern peatland ecosystems to increases in temperature and exposures to elevated atmospheric CO2 concentrations."

@jeffbaumes , @mcovalt , @dwinston What do we need to do to fix this?

dwinston commented 2 years ago

It was unfixed in the nmdc-runtime store (mongodb). I submitted a changesheet to fix, i.e.

id action attribute update
gold:Gs0110138 update description This study is part of...

to /metadata/changesheets:submit.

Looks like it took: https://api.dev.microbiomedata.org/studies/gold:Gs0110138

Now the nmdc-server team can ingest.

pvangay commented 2 years ago

FYI via email from @jeffbaumes, we should hold off on ingests until @mcovalt is back from vacation. Hopefully we'll see the changes after that.

mslarae13 commented 2 years ago

@ssarrafan I'd like to check in on this at the infrastructure sync today (10/20)

ssarrafan commented 2 years ago

@ssarrafan I'd like to check in on this at the infrastructure sync today (10/20)

Sure I'll add this to the agenda.

mslarae13 commented 2 years ago

Matt started an ingest. @mcovalt can you let me know when dev is good / you're ready for me to check SPRUCE

mcovalt commented 2 years ago

Ingest is still ongoing. I'm debugging why the ingest has still been stalled. I'll update next week on the current status.

mslarae13 commented 1 year ago

Reassigning to @naglepuff

naglepuff commented 1 year ago

This is fixed in dev. https://data.dev.microbiomedata.org/details/study/gold:Gs0110138

mslarae13 commented 1 year ago

Yup, once it's been updated on prod we can close this issue. Any idea when that might be?

ssarrafan commented 1 year ago

I'm removing this issue from the sprint since the work is done pending push to prod.

aclum commented 1 year ago

We'll check on this once data portal prod is updated. Added this to GSP board and the current sprint.

aclum commented 1 year ago

Expect data portal prod ingest to happen tomorrow.

aclum commented 1 year ago

Fixed by prod data portal ingest this AM.