amphibiaweb / amphibian-disease-tracker Goto Github PK

After #17, #10

Sample dataset:

37.877, -122.289
37.878086, -122.290059
37.878511,-122.288033

ARGH WHERE IS THE LINK

page to show visually (a map) all the project transects as well as being able to search for projects by species, by pathogen, state, and users.

This touches on #3

Yikes!

Berkeley is clearly not 10e6 meters in radius

Allow some spatial footprint for Projects prior to datasets being uploaded. This will allow users to see future intentions of field work and facilitate planning and coordination.

See Issue #3

Blocks #5 , since we need a way to check!

troubleshoot the registration process since it was not clear to users that they had a password that does not meet requirements

Mike Adams articulated a need we intend to create by making the mapped data the central focus of the Portal-- specifically to be able to map or model sampling effort and aid in prioritization of "where we most need sampling given where we have results, where people already intend to sample, and the risk models."

So potential two issues here: map sampling efforts to reveal gaps and aid in risk modeling and show where current activity is (active field efforts) See Issue #3

Use case: accession code or recordlevel GUID or both for citing in publications. May need community feedback about which is priority (one or the other or both).

Using FIMS will allow us to mint a doi/ark for this purpose but maybe we also need a sequential GUID? Would this require ADP to use the FIMS uploader then?

More discussions with Deck needed.

From Dede Olson: To facilitate cooperation and coordination, let users indicate time and places or taxa they are planning to do field work or sampling so people can contact each other to coordinate or do complementary (non- redundant) work.

Brings up issues of how to manage such a community so we should seek ways to integrate networks or platforms people already use (eg. Google +, Google Maps, Twitter, etc-- not suggesting these but as examples). Possibly offsite or light API integration.

Not sure why but link in "" goes no where even though I updated to point to this repo.

Not sure if this is known but not working! (either with link or manual input of codes, neither works)

Reminder to embed RSS into a jekyll page (maybe with this: https://github.com/snaptortoise/jekyll-rss-feeds)
https://api.zotero.org/groups/419428/items/top?start=0&limit=25&format=atom&v=1

Separating out the functions of Project creation and uploading makes the most sense for us. We should also have a link to the FIMS site where we should make clear that a upload template can be made. (E.G. here: http://biscicol.org/biocode-fims/templates.jsp or another dedicated page? I (@mkoo) will have to ask Deck about that once we get our final template to him)

Uploading your project data

Need to add a link to the FIMS site where users can create their own template for data. The text here should indicate that the uploaded file needs to conform to the FIMS-generated file with the appropriate header row and name fields.

We decided that this form should be ONLY for Create Project so just a link to a new form for Uploading-- see below suggestion for "Edit or Add to Existing Project" #21
…

-Data Parameters - confused about what is being asked for here?

-- this can be on the separate upload form now.
-- BTW The Preview of the data is great!
…

Do as home.html initially, but at least have something in place to eventually become a new index

must have real lat/long

@mkoo , @JoyceGross

Add yourself to the keyring as per this link. When you've done so, I can re-encrypt the files for your guys.

Right now, REST endpoint takes .xls, .xlsx, and .csv. Will need to meet with John Deck to work out the implementation specifics.

Extension of #21 , just making little steps.

Is it too early to consider OpenAuth? (http://oauth.net/)
Maybe even Google Sign-in --https://developers.google.com/identity/

major (obvious) considerations:

• security
• ease for user to use a pre-existing authentication
• reduces the 'casual' registered user

Such as:

• JSFUCK
• Heiroglyphy
• resume.js ?

View which projects have:

• datasets attached
• users affiliated with project

in edit mode:

• indicate which fields are editable in project

Also view:

• general users admin and their projects or datasets
• allow changing users permission
• Total user list

On Thu, Dec 10, 2015 at 11:52 AM, Michelle Koo [email protected] wrote:
HI all, thanks for portal input yesterday!

OK, I want to discuss the project workflow before I start filing issues. Here's a run down of my >questions on some of the details. Please weigh in with your thoughts or suggestions.

The first step is going to functions under the button [+Create Project]

• enter in contact info here or under your user name??? probably here... but let me know what you think
• "Project Lab" not sure what this would be unless the lab is under an agency, if the latter, should be controlled vocab so a pick list is needed.

Feedback: Keep both fields as they may indeed be separate things -- we had some examples, especially if an agency lab or if the lab is just doing the lab tests. Project PI and Contact may also be different (e.g. advisor and grad student will be different names)

• change "Project Lab" to "Diagnostic Lab"
• For the Field"Disease Studied"--> for now keep it simple dropdown menu of chytridiomycosis | other
• "Pathogen" maybe user submitted but with tool tip " Bd or Bsal or other"

"Project Notes" -- maybe make clear that this is for a VERY brief abstract

• maybe include tooltip: "Project notes or abstract"

-"If you don't enter anything, we'll guess from your dataset." I would edit this to:

• "Leave blank for a bounding box to be calculated from your sample sites" this is more clear
• Need a "REady to Submit" button instead

allow updating of personal or lab URLs, emails, address, bios(?)

See GRRS for example terms and disclaimer

Future Discussion item

re: recaptcha

Also make toggle danger red!

Replace term 'Transect' with 'Planned Target Area' for a polygon or boundingbox.

Include option to generate bounding box from uploaded records.

-- tool tips for uncertainty (eg. GPS coordinates should be 30 m default or less)
-- maybe links for mapping
-- tips on making data as useful as possible (e.g more than 4 digits in DD, etc)

More thoughts on Permissions: really two layers are needed. Permissions for the Project (edit rights, upload rights, private/public) and recordsets the latter (private/public is inherited to the record level). should we allow record level editing?

Opening an issue for an on-topic discussion of this!

My initial plan was binary permissions (true/false), but if we want to go more granular, HOW granular? Just another "superuser" role = another column/attr? Or enumerated permissions?

• Read
• Edit existing data
• Edit, add, or delete metadata
• Add data
• Delete data
• Change permissions
• Change users (Add/Remove users onto project)
• Export data

If enumerated, we should then decide certain role categories with buckets of permissions.

Maybe distinguish admin vs. project with, eg, foo!admin

a reminder of this requirement and that AW exports a taxonomy list every night here:
http://amphibiaweb.org/amphib_names.txt

EG, ping iNat for out-of-range in uploaded data

specifically for a Project

This would let us resolve individual samples

Portal could function as a site to aid matching people with money for PCR with people who are willing to collect samples and labs able to do the work with the correct protocols. We've discussed this from simple lists to more complex searching/matching functions.

Mike Adams suggests that there is a need to aid "entities (who) want to pay for some surveillance work but can't decide how to do it. Some would like to use their funding to encourage people to sample in high priority areas. " He is also interested in integrating decision support needs. Likely this kind of modeling or analysis is out of scope for the Portal but we could create datasets or web services to support other tools or sites.

From Maria Forzan: she suggests a data integration-- CWHC (formerly CCWHC, Canadian Cooperative Wildlife Health Centre) has a database that records mortality reports in all wild species across Canada. At least data discovery on both portals? Contact Maria to set up discussion with their IT/Programming team.

Edit Existing Project

• will users be able to add a CSV to an existing project here? If so, let's change the button to read "Edit or Add to Existing Project". Otherwise I suppose files can only be added under the first button, which we should then modify the above. I think I prefer having the former to separate the project creation aspect with the upload and associate functions.

• we may need a permission layer so that only some users can edit a Project while others can upload files and associate to it.

More thoughts on Permissions: really two layers are needed. Permissions for the Project (edit rights, upload rights, private/public) and recordsets the latter (private/public is inherited to the record level). should we allow record level editing? (See #22)

To Do for this issue:

• Load up all editable data ( #26 )
• Populate all editable fields
• Manage users for a project
• Write the saving handler

As opposed to just the listing of #24

Not actually edit yet, mind, just show it. Baby steps.

Included basics, plus

• Basic bounding geography
• ARK identifier (resolver: https://n2t.net/ )
• ?? more??

• Where geographically have tests been made for Bd, Bsal, or both? Where has Bd or Bsal been detected? (See #118)
• In which species have Bd or Bsal been detected? (See #118)
• Where has presence of Bd or Bsal never been tested? Where has Bd or Bsal never been detected?
• When, where and in which species was the first recorded occurrence for Bd or Bsal? (this may also be a literature review task)
• Which species have never been known to be exposed to Bd/Bsal? Do they exhibit any traits that may make them vulnerable, including proximity to known outbreaks, or correlations to habitat or life history traits that make them vulnerable?
• How have the distribution, prevalence and intensity of Bd/Bsal changed over time and space?