Content comments for biorepo portal redesign

[kyule]

Brackets indicate suggested additions, deletions, or edits to text.

• About samples page: The NEON Biorepository publishes occurrence records for every archived sample and specimen, as well as additional value-added sample-associated data not present in NEON data products [in the sample portal] and makes these samples available for loan.
• Sample Repositories page: (1) I noticed a couple instances without a comma before the "and" at the end of a list... I personally have a semi-strong preference that those be included. Nitpicky but it slows down my comprehension of a sentence. (2) Part about LMZ: At least historically, this is not the only pathogen testing lab (and it's not mentioned that they test other things) so I think it's awkward to include here unless NEON really wants to. (3) All tick voucher specimens collected by NEON during construction and continuing through [field year 2023] are available and will be curated through the U.S. National Tick Collection at Georgia Southern University. [All tick genomic extracts and tick specimens collected in 2024 and beyond are available from the NEON Biorepository.] (4) Megapit samples.... odd because only the distributed initial characterization samples are in MI. The megapit samples are actually at NEON HQ and will move to ASU after renovations... (5) Assignable Assets --> Research Support Services (6) "previously collected in Florida" --> previous to what? I think 2018 but idk (7) MSB is duplicated in the list (8) Carnegie/Essig, super not a true statement, I would update to just 'taxonomic reference specimen collections' (9) Questions about samples not housed at the NEON Biorepository at [Arizona State University] should be sent directly to those repositories. --> i.e. replace the part "to the NEON Archival Samples Team." .. I think that form is dead or at least the link doesn't work (10) Hawaii - move to the above section and specify it's only voucher specimens collected prior to ~2023
• Sample services page: (1) [Loans of e]ndangered taxa, fragile specimens, or samples which are deemed to be in limited supply [may be subject to more stringent review]. (2) Assignable Assets --> Research Support Services and link
• Dataset publishing page: (1) Published Research Dataset --> Goes to "old" page format and seemingly Has not been integrated yet Can we bundle with checklists like "Research Datasets and Checklists"? (2) Delete this: These sample lists will be published to the Environmental Data Initiative portal, increasing the visibility of sample use in researhc. (3) such as the Global Biodiversity Information Facility (GBIF) portal[,] further increasing their visibility to the broader research community.
• Sample analysis page: (1) Rest API explorer link not active (2) [To track samples moving between facilities, ]NEON generates shipment manifests and standardized receipt forms that enable NEON to track the location of a sample through its lifetime from generation in the field to final disposition. (3) Screenshot from the sample explorer actually doesn't have any shipment or location data displayed because it represents the tagged mammal and not any samples, so that is a bit confusing in the context of the above text IMO
• Checklists page: I know you know but this is the one super obvious place images need to be switched.
• Search results page: (1) "Occurrence Records" tab easily gets cut off depending on the window size (2) recommend a note saying the number of images at the top like is done on the species list tab especially since if there are none since it seems like the page just isn't loading or something (3) maybe known issue for some other reason, but the maps don't load
• Main landing page: Not sure where those stats come from, since some are not correct (species count, years, and probably images)
• Maybe I missed it, but IMO Symbiota and BioKIC homepages should be linked somewhere
• Will the management tools and sitemap etc show up when we are able to log in? Will they essentially look the same as before?

[sunray1]

• Search results tabs are not changing into tabs
• Update jquery in /neon/ code (this was updated in 3.1)
• image tab in list.php is missing?
• Look into css issues (various buttons and links are weird); see also tables in manifestviewer.php formatting
• collections/map/googlemap.php not loading
• public full records throwing array errors (collections/individual/index.php?occid=1052607)
• fix collections links in list.php to go to neoncollprofiles.php
• class error in https://biorepo.neonscience.org/prodreview/collections/misc/neoncollprofiles.php
• Move 'add checklist' from my profile to sitemap
• Deprecated: Function utf8_decode() is deprecated in /var/www/html/neon/prodreview/classes/OccurrenceSesar.php on line 516 when getting IGSNs
• make API a larger button on https://biorepo.neonscience.org/prodreview/misc/sampleanalysis.php
• add missing breadcrumbs in sitemap
• Warning: Undefined array key "obs" in /var/www/html/neon/prodreview/imagelib/contributors.php on line 67 on https://biorepo.neonscience.org/prodreview/imagelib/contributors.php
• update sample search link in About samples page
• manifest list is very wide in manifest viewer
• change collection link in harvester to neoncollection links
• firefox is not showing sidebar and breadcrumbs
• Symbiota white text in the header
• check social media and see if we have our own
• text in about samples needs to be fixed
• updateBreadcrumbHash in head.php is not working
• add popup for login about biorepo logging in

[sunray1]

CSS Issues

• Fix home page stylings(blue bar, hero text, buttons, space when blue bar is moved over)
• Statistics needs to be white
• Change buttons to look like NEON blue buttons
• taxa/index.php?tid=80799 - results tab should be white
• https://biorepo.neonscience.org/prodreview/sitemap.php - fix headers
• Xs in https://biorepo.neonscience.org/prodreview/neon/search/index.php
• tabs in https://biorepo.neonscience.org/prodreview/collections/misc/browsecollprofiles.php
• button overlay in https://biorepo.neonscience.org/prodreview/collections/misc/neoncollprofiles.php?collid=50
• buttons on list search results need to be square - https://biorepo.neonscience.org/prodreview/collections/list.php?taxa=Aedes
• css issues on https://biorepo.neonscience.org/prodreview/collections/misc/collstats.php
• Fix buttons in NEON header
• https://biorepo.neonscience.org/prodreview/collections/misc/collpermissions.php?collid=54 - weird css
• fix hero images on subpages to be full width

[kyule]

@sunray1 Noticed a quirk related to logins in order to submit receipts and other tables (https://data.neonscience.org/web/external-lab-ingest) we have to be logged into the NEON site as [email protected] instead of ourselves so we have to log out and log back in as biorepo to submit. My biorepo management access seems unchanged (it still calls me kyule when I start a session for example), but "my account" is Bio Repo for the overall neon site. Not sure how much of an issue this really is, but maybe there is a simple workaround...