Plone 5 Transition

This document tracks the status of the Plone 5 transition for the EDRN Public Portal.

In the tables below, the columns are as follows:

• Dev: a mark here indicates the developers (SK, DL) believe the feature is complete.
• QAc: no mark here indicates the quality assurance check (HK, MC, others) confirms the feature is complete.

The latest portal software is available at:

https://edrn-new.jpl.nasa.gov/portal/

Theme and Window Dressing

This section tracks the status of stylistic and non-content elements.

Item	Dev	QAc
LDAP Integration
Anonymous browswing	O
Regular user login	O
Site manager login	O
Header
Luggage tag logo	O
Log in/personal link	O
Search box	O
Removal of DCP text	O
Footer
White background	O
Section 508 Links	O
NIH Motto	O
Classic look-and-feel
Helvetica or other sans-serif font	O
Gray navigation bar tabs	O
Button-style Quick Links	O
Except for new (not old) home page image	O

Portlets

This section tracks progress on the portlets for the site.

Quick Links Portlet

This subsection tracks progress on on the Quick Links (left side) portlet.

Item	Dev	QAc
Network Consulting Team link	O
Informatics link	O
Groupss link	O
Public, Patients, Advocates link	O
Funding Opportunities link	O
Sites link	O
Member Directory link	O
Standards link	O
DCP link	O
CBRG link	O
Bookshelf link	O
Remove informatics standards link	O

DMCC News Portlet

This subsection tracks progress on on the DMCC News (right side) portlet.

Item	Dev	QAc
RSS Feed	O
Two News Items Displayed	O
Spacing issues	O

Static Content

This section tracks the progress of the static (non-RDF periodically updated) content.

Item	Dev	QAc
Network Consulting Team	O
About EDRN	O
About EDRN YouTube video	O
Resources	O
DABS link incorrect - probably	O¹
Video links incorrect - should move to YouTube	O¹
Informatics	O
Informatics YouTube videos	O
Public, Patients, Advocates	O
Funding Opportunities	O
Bookshelf	O
Collaborative Opportunities	O
404s on Informatics page¹

¹This mimics the current operational behavior and is not dependent on software. Because we're using a content management system, We can alter the content any time after the P5 release.

RDF Data

This section tracks completion of data that (usually) comes from the DMCC in the form of a SOAP API translated into RDF (although not always) and then ingested into the portal.

Biomarkers

Item	Dev	QAc
RDF ingest	O
Biomarker-Organ-level security	O
Statistical graphics	O
Facet search	O
Tabuluar listing (biomarker, type, organs)	O
Show type "panel" on list	O
Searching by alias named	O
Pagination	O
Elemental biomarkers	O
Biomarker panels	O
Biomarker basics tab	O
"3" in attribute boxes	O
Short name always blank	O²
Biomarker basics formatting	O
Biomarker organs	O
Biomarker studies	O
Biomarker publications	O
Biomarker resources	O
Biomarker datasets (see 8-gene-panel-for-barretts)	O
Privileged access to non-public biomarkers	O
Smaller yet wider attributes box	O
Going "back" makes tabs appear as links, not tabs (can't repro)	X§
HGNC links on Resources tab of a biomarker aren't working	O†
Gene,UniProt,GeneCards, etc. links on Resources intermediary pages	O
Hyperlink to Informatics Center email if you're not logged in	O¶

§Cannot reliably reproduce; reported to upstream developer. This is a window-dressing issue, though. The tabs may be gone but the hyperlinks still work; no information is lost. Reloading the page brings the tabs back—not the end of the world.

²The BMDB's MySQL database has a table called biomarkers with a column shortName which is blank for all 940 rows. Once this is populated and new RDF is generated from it, then short names should start appearing.

†Note that the 234 URLs given by the Biomarker Database use an older genenames.org format (6 use the newer format), so this isn't a portal problem.

¶Already there, just wasn't being underlined.

Protocols

Item	Dev	QAc
RDF ingest	O
Tabular listing (title, abstract, investigator)	O
Sorted results	O
Pagination	O
u' and ' appearing	O
Protocol title	O
Protocol abbreviated name	O
Protocol abstract	O
Protocol aims	O
Protocol analytic method	O
Protocol comments	O
Protocol biomarkers	O
Protocol datasets	O
Protocol lead investigator	O
Protocol coordinating investigator	O
Protocol involved investigator	O
Protocol sites	O
Protocol biomarker name	O
Protocol design	O
Protocol field(s) of research	O
Protocol collaborative group text	O
Protocol phased status	O
Links to investigators	O

Science Data

Item	Dev	QAc
Global nav label "Data"	O
RDF ingest	O
Statistical graphics	O
Graph missing labels (works for SK)	?
Facet search	O
Sorting on facets	O
Sorting on results	O
Tabuluar listing (title, pi, organ, protocol, collaborative group)	O
Pagination	O
Linking directly to eCAS	O
Transition to LabCAS (awaiting review)
Misspelled ingest data researchSupprot	O
Graph bars too wide and require horizontal scrolling 😱	O
Incredibly annoying graph (change wording, overlapping names) 😱	O

Publications

Item	Dev	QAc
RDF ingest	O
Show publications	O
Click on publication ID don't go anywhere; nice to go to pubmed³	O
Statistical graphics	O
Search text	O
Advanced search filters	O
Sorting on results	O
Tabular listing (publication, journal, year)	O
Pagination	O
Publication title	O
Publication authors	O
Publication abstract	O
Publication PubMedID	O
PubMedID link	O
Publication volume appearance	O
Rabies publication from 1975? (bad DMCC data⁴)	O

³From email feedback: publications section: When you click on the publication id you don’t go anywhere. Would be great if this can take you to pubmed for that id ☺.

⁴The DMCC says eSIS publication 794 is titled "Nuclear matrix protein alterations associated with colon cancer metastasis to the liver" and is from 2002, but we ignore all DMCC data except for the PubMedID, which for that publication is 1237467. When we pull data from PubMed, 1237467 is indeed "[Rabies vaccination with regards to its epidemiology (author's transl)]", 1975. Upstream data should be fixed rather than making a special check in the portal. P4 was rife with special cases for handling bad upstream data; let's keep P5 clean—and fix the gosh-darned upstream data!

Sites

Item	Dev	QAc
RDF ingest	O
Sorting based on site type	O
Inter-page jump to site type section	O
BDL organ sorting	O
BDL abstract title and excerpt	O
Investigators linked on sites page	O
People
Principal Investigator	O
Co-Principal Investigators	O
Co-Investigators	O
Investigators	O
Protocols on investigators	O
Publications on investigators	O
Staff ID display	O
Peons on staff view	O
BDLs have lost organ and project summary information	O

Group Workspaces

Item	Dev	QAc
RDF ingest	O
Committees workspaces	O
Committees preserved files	O
Collaborative groups	O
Collaborative preserved files	O
Links to Biomarkers, Projects (Protocols), Datasets	O
Fix mucked up projects & protocols on collaborative groups	O
Highlights	O
Misspelled "Collaborive"	O
Sort related link	O
Subsequent RDF ingest makes groups work	O

Usability Study

Item	Dev	QAc
Move "About EDRN" to last in navbar	O
"DMCC Site" next to login	O
"Protocol" → "Associated Protocol" on Science Data	O
"Title" → "Name" on biomarkers	O

Miscellaneous

Item	Dev	QAc
Automatic periodic ingest	O
Automatic periodic ingest in Docker environment	O
Hidden errors during ingest	O
Login disclaimer
Super Users with Super Powers	O
Contact info CAPTCHA	O
Global nav order: Home Biomarkers Protocols Data Pubs Resources	O
Sort on in faceted listings: remove or improve (removed for now)	O
Search
Free text search	O
Ranking of biomakers in results	O
Filtering on search results	O
Sorting on search results	O
Heather's search results‡	O
Heather's feedback 2019-11-20	O
Heather's additional search indexes 2019-11-27	O

‡doesn't return same results as portal at NCI. If I search for "Marks" I see only 2 of his protocols on P5 site. I see 5 on NCI site. If I search for a specific protocol id "447" - I get no results returned on P5. I see a protocol on NCI site. I also get discrepancies when searching "Heine".

For "Heather's feedback 2019-11-20" above, these refer to the following:

Informatics Portlet - https://edrn-new.jpl.nasa.gov/portal/informatics :
    - Tools section:
         - Biomarker Database Link- we should remove this or link to biomarkers tab on Portal (this is also a link under Data - so maybe we should just delete this).
        - EDRN Specimen Exchange - we should remove this.
         - REDCap - we should remove this.
         - Statistics - do we want to link to COMPASS at Fred Hutch? - https://www.fredhutch.org/en/research/divisions/public-health-sciences-division/research/biostatistics/comprehensive-center-for-advancement-scientific-strategies-compass.html
    - Data section:
             - Specimens - remove link
         - Science Data - link is broken - fix link (change to just data)*
    - Standards section:
            - EDRN Standards - remove link and figure out what to do in next version
    - Publications section:
             - these two links are broken:*
        Crichton DJ, Kincaid H, Kelly SC, Srivastava S, Hughes JS, Johnsey D. Creating a National Virtual Knowledge Environment for Proteomics and Information Management. Informatics in Proteomics, Srivastava S (ed.) 2005.
        Mattmann CA, Crichton DJ, Hart AF, Goodale C, Hughes JS, Kelly SC, Cinquini L, Painter TH, Lazio J, Waliser D, Medvidovic N, Kim J, Lean P. Architecting Data-Intensive Software Systems. Handbook of Data Intensive Computing, Furht B, Escalante A (eds.) 2011.
        - Leadership section:*
        - The JPL hyperlink goes to eCAS, should go to JPL site (https://edrn-new.jpl.nasa.gov/portal/sites/128-nasa-jet-propulsion-laboratory ). We should also add a link to the Fred Hutch - to go to their site (https://edrn-new.jpl.nasa.gov/portal/sites/5-fred-hutchinson-cancer-research-center )

Groups and Committees:
    - Breast/GYN - https://edrn-new.jpl.nasa.gov/portal/groups/breast-and-gynecologic-cancers-research-group **
        -The highlights aren't showing up (there should be 6).
        -Calendar - Past Events - these are missing.
        -Documents - one of the documents - OC Team Project January 2013 Teleconference Minutes - should be private, but shows up when I'm not logged in.
    -GI - https://edrn-new.jpl.nasa.gov/portal/groups/g-i-and-other-associated-cancers-research-group **
        -The highlights aren't showing up (there should be 7).
        -Calendar - Past Events - these are missing.
    -Lung - https://edrn-new.jpl.nasa.gov/portal/groups/lung-and-upper-aerodigestive-cancers-research-group **
        -The highlights aren't showing up (there should be 10).
        -Calendar - Past Events - these are missing.
    -Prostate - https://edrn-new.jpl.nasa.gov/portal/groups/prostate-and-urologic-cancers-research-group **
        -The highlights aren't showing up (there should be 7).
        -Calendar - Past Events - these are missing.
    -Steering Committee - https://edrn-new.jpl.nasa.gov/portal/groups/steering-committee **
        - Calendar - Past Events - these are missing.


-Funding Opportunities Portlet:
    - Assistance Mechanisms for your Biomarker Research -*
        - Request for biomarkers link broken. Here's the working link from NCI Portal - https://edrn.nci.nih.gov/colops/request-for-biomarkers.pdf

Data Tab
    - The graph isn't showing Lung datasets.

*I understand we can update the content after the release.
**I know this is also content, but I think it's too much to fix after release.


New issues or updates for next version:
- For biomarkers that are not public. Change contact from heather Kincaid to IC Portal Team - [email protected]

- When clicking contact on footer - https://edrn-new.jpl.nasa.gov/portal/biomarkers/muc1 There's no way to get back from this form. Even if you complete form.

-Groups and Committees Portlet:
    Committees:
    We should revisit what we are showing under committees. Most have only a members list. Many are duplicates of what's on sites portlet and the sites portlet has more info. Also, many don't meet anymore. We should ask Christos if we can delete many of these. Maybe we only need to keep Steering Committee?