Closed nutjob4life closed 1 year ago
@hoodriverheather I have a prototype here:
https://edrn-dev.jpl.nasa.gov/portal/renaissance/data-and-resources/metadata-collection-form/
Since there's no CAPTCHA, I think we should require a login to access it. If it needs to be open to the public, we'll add a CAPTCHA.
Some differences from your wireframe:
OwnerPrincipal
MethodDetails
so I added one.cfg
file: ref URL, ref URL description, DOI, DOI URL.When you hit Submit, the portal generates a collection-level .cfg
file and emails it. Right now the email goes to you and me while we test.
@nutjob4 sorry for the delay on looking at this! I'm just trying to get to the dev portal and getting an error - "Internal Server Error". Can you let me know when it's back up?
Goodness gracious, no apology needed ๐
The site is back up: https://edrn-dev.jpl.nasa.gov/portal/renaissance/
@nutjob4life It's looking good! I wonder if we could provide pick list values in the form right now for the items that are coming from KDSB? Eventually we could decide to pull from KSDB if people really use the form :) I really like the description text that you have on some of the items. I'll take a closer look to provide descriptions for some of the other fields. Do you think you could create the .cfg using Asitang's key value pairs? We haven't done this yet in LabCAS, but it how we want to move forward.https://github.com/EDRN/labcas_publish/commit/a02c1a7d7b1f6c7ffe1215d775993eb3c746d83a
@hoodriverheather You got it!
If you can tell me the current permissible values in KSDB, I can put them in. (I tried logging into KSDB but neither my EDRN nor my Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions passwords work).
As for @asitang's key-value pairs, could you tell me which lines need to change?
[Collection]
CollectionName = Heather Test
CollectionDescription = This is a test collection description.
Discipline = Genomics
DataCategory = RNA Sequencing
Institution = NASA Jet Propulsion Laboratory
InstitutionId = 128
LeadPI = Crichton, Dan
LeadPIId = 1075
DataCustodian = Heather Kincaid
DataCustodianEmail = heather.kincaid@jpl.nasa.gov
Organ = Blood
OrganId = 2
CollaborativeGroup = lung
Consortium = EDRN
ProtocolName = Standard Specimen Reference Set: Prostate
ProtocolId = 120
Species = Homo Sapiens
OwnerPrincipal = cn=JPL,dc=edrn,dc=jpl,dc=nasa,dc=gov|cn=DMCC,dc=edrn,dc=jpl,dc=nasa,dc=gov
I read over that link, but I don't understand what it's supposed to be (and why aren't you guys just using RDF subject URIsโฝ).
So instead of
ProtocolName = Standard Specimen Reference Set: Prostate
it's supposed to be
ProtocolName = Protocol_ProtocolID_120
Is that right? What other lines above are affected? ๐คทโโ๏ธ
@nutjob4life Here's the list for Discipline: Genomics Proteomics Pathology Images Radiology Immunology Pathology Undefined
Here's the list for Data Category: Sequencing RNA Sequencing DNA Methylation Sequencing DNA Microarray Analysis Mass Spectrometry Whole Slide Imaging Tissue Micro Array Immunohistochemestry CT MRI Mammography Fluoroscopy PET Documentation Biospecimen Clinical Immunoassay ELISA Luminex LabMAP Protein Microarray Single Slide Image Multiplex-Immunoflourescent Staining Radiomics Antibody Microarray
This google sheet actually has more current values than KSDB. https://docs.google.com/spreadsheets/d/1jvoSqXNupkV6T7Ptn7vtH2Iszx09sWvysRb8q8nSSpw/edit#gid=0
As for the key value pairs. It would be best to ask @asitang the format of the values and why we aren't using RDF subject URIs. I think we would use this for the following: Institution, LeadPI, Organ. Any pick lists.
Thanks @hoodriverheather! I used the Google Sheet in order to the latest-and-greatest for Discipline
and DataCategory
. While there, I also grabbed Species
.
Two things:
MethodDetails
on the Google Sheet; can we drop this box?DOI URL
with a space in it; is that correct?Woops, that three things ๐
Anyway, please see https://edrn-dev.jpl.nasa.gov/portal/renaissance/data-and-resources/metadata-collection-form/ for the latest.
@nutjob4life Thanks for catching all of these!
I realized after filling in the form the following:
Please check out the latest dev form.
Next questions I have:
@hoodriverheather please check out the open questions โ when you get a chance ๐
@nutjob4life here are answers to the above questions:
@hoodriverheather to QC this:
@nutjob4life This is sooooo close.
What about adding the following text to the science data page. If you have data you would like captured or linked in LabCAS, please complete the Metadata Collection Form. Or contact the Informatics Center with any questions.
I'm struggling with what to call the Reference URL and the Reference URL Description. Users never understand what this field is. How about: Change the label of Reference URL to URL link and change the description to: Optional URL link to external or additional data described by this collection. WDYT?
@hoodriverheather okay here's how the Data page could look:
That look all right? The "Informatics Center" is a mailto:
link to ic-portal@jpl.nasa.gov
.
For the form itself, I used your suggested text:
Does that look okay? Should the "Reference URL Description" change too?
@nutjob4life I think that looks great! Thanks!!
@hoodriverheather okay, sending to edrn-dev
@hoodriverheather to QC this:
This looks great!! ๐
See https://app.diagrams.net/#G1P7zvvPydbZ08-epAvsg_vZUL0Wgz_AwS