Erin's minor issues with latest contouring Oceano App

[bbest]

shiny.calcofi.io/oceano

From @evsatt...

A few minor thoughts from initially playing around with it:

• [ ] 1. Can the depth bin have 0-5 possible (or maybe type in min/max)? Right now, I think the 'min' range that you can get is 0-30m but might be nice to be able to get the surface layer.
• [ ] 2. Is there a way to add a 'thinking' timer or some other way to indicate that the app is updating? I can't quite tell when its done updating -- there is no indication that the app is working when I click update (e.g., for the longer time periods it doesn't update - or maybe takes a long time?)
• [x] #11
• [ ] 4. We have nutrients, chla, and a few other variables in the hydrographic data -- how difficult would it be to include those in the drop down menu also?
• [ ] 5. Is there a way to integrate the sampling effort back into the map? I thought that was a really useful feature.
• [ ] 6. I sometimes am getting a HTTP ERROR 502 and a "socket hang up" -- not sure if those are random or a deeper bug
• [x] 7. Is the data updated in the app? Does it pull from the database or a static file at this point?
• [x] 8. Trying to download the data gives me a "failed server" message and the tiff is a black and white image of the land/ocean (without the points). The map points was giving me the error. Is there a way to have an image output that can work in mac preview?
• [ ] 9. Too much data for spatial and temporal extent, eg historical 1970 to present.

[bbest]

1. Can the depth bin have 0-5 possible (or maybe type in min/max)? Right now, I think the 'min' range that you can get is 0-30m but might be nice to be able to get the surface layer.

We could add text boxes to explicitly set the min and max. The issue is real estate on the user interface, which might be better served with an interface that opens a much more expansive modal dialog window (similar to the Area button now) to specify all the query parameters. Then we could have each query parameter on its own dedicated tab, like Depth, Time, etc.

[bbest]

2. Is there a way to add a 'thinking' timer or some other way to indicate that the app is updating? I can't quite tell when its done updating -- there is no indication that the app is working when I click update (e.g., for the longer time periods it doesn't update - or maybe takes a long time?)

Good idea! Yes there are progress indicators we could add like here:

• Shiny - Progress indicators

It might be hard to estimate how long it will take. For that matter, we should probably place limits on how much data it can crunch on, eg limit total number of observations and reduce time/space parameters.

[bbest]

3. Any chance the update button can be on the bottom on its own more and maybe a more noticeable color (it took me a second to initially find it)?

• make Update button more noticeable · Issue #11 · CalCOFI/apps

[bbest]

4. We have nutrients, chla, and a few other variables in the hydrographic data -- how difficult would it be to include those in the drop down menu also?

Let's look at this together with @mfrants to identify the fields and tables. Theoretically it shouldn't be hard to add.

[bbest]

5. Is there a way to integrate the sampling effort back into the map? I thought that was a really useful feature.

Yes, we should discuss how best the sampling effort could be displayed, since it could be too busy if spanning many years. I would like add the option to visualize the points or raster too. It would also be cool to setup a time slider along the bottom with a play button so you can see a variable evolve over time.

[bbest]

6. I sometimes am getting a HTTP ERROR 502 and a "socket hang up" -- not sure if those are random or a deeper bug

Can you let me know if you notice any patterns of terms when seeing this?

I should definitely add some logging to figure out who (IP address) is pressing what and possibly restore a previous query with a bookmark:

• Record logs in shiny apps • shinylogs
• Shiny - Bookmarking state

[bbest]

7. Is the data updated in the app? Does it pull from the database or a static file at this point?

The data comes from the database directly, except for the polygons and raster of the Map tab, which get cached based on a hash generated from all the input arguments in get_map_data(). This speeds up performance significantly, but I should add another argument with a date the database was last updated so it regenerates if outdated by newer data in the database. It does update the idw_stats table here so we can cleanup unused outputs (.geojson, .tif).

[bbest]

8. Trying to download the data gives me a "failed server" message and the tiff is a black and white image of the land/ocean (without the points).

Which link? Map points (.csv) or Time series data (.csv) or ...

The raster (*.tif) will look like a black & white image in most non-GIS image previewing apps, like Mac Preview:

Preview on Mac

(I actually see the outline of the raster extent with values, but weirdly the screenshot doesn't work here.)

QGIS

R

library(terra)

r <- rast("/Users/bbest/Downloads/idw_ffefc04c.tif")
plot(r)

[evsatt]

Yes I will keep a look out for patterns :)

On Mon, May 1, 2023 at 1:07 PM Ben Best @.***> wrote:

6. I sometimes am getting a HTTP ERROR 502 and a "socket hang up" -- not sure if those are random or a deeper bug

Can you let me know if you notice any patterns of terms when seeing this?

I should definitely add some logging to figure out who (IP address) is pressing what and possibly restore a previous query with a bookmark:

• Record logs in shiny apps • shinylogs https://urldefense.com/v3/__https://dreamrs.github.io/shinylogs/articles/shinylogs.html__;!!Mih3wA!CcYL4QBrDpKhrQzeFsLjvHmfRhwDZskHbcR3Ja4libgx7Gn4_MsNX1geDLxLQGuMkGNtFYyK2L4EKAzp5f1WUzOKyte1Sw$
• Shiny - Bookmarking state https://urldefense.com/v3/__https://shiny.rstudio.com/articles/bookmarking-state.html__;!!Mih3wA!CcYL4QBrDpKhrQzeFsLjvHmfRhwDZskHbcR3Ja4libgx7Gn4_MsNX1geDLxLQGuMkGNtFYyK2L4EKAzp5f1WUzMWJXSbCg$

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--

Erin Satterthwaite | she/her
Marine Ecologist & Sustainability Researcher
CalCOFI Program Coordinator
UC San Diego - Scripps Institution of Oceanography
California Sea Grant & CalCOFI
9500 Gilman Dr., La Jolla, CA 92093-0232
*work: *(858) 333-7265

*Play is the highest form of research *
                                 *   ~Albert Einstein*

[evsatt]

The map points was giving me the error. Is there a way to have an image output that can work in mac preview?

On Mon, May 1, 2023 at 1:26 PM Ben Best @.***> wrote:

8. Trying to download the data gives me a "failed server" message and the tiff is a black and white image of the land/ocean (without the points).

Which link? Map points (.csv) or Time series data (.csv) or ...

The raster (*.tif) will look like a black & white image in most non-GIS image previewing apps, like Mac Preview: Preview on Mac

[image: image] https://urldefense.com/v3/__https://user-images.githubusercontent.com/2837257/235523876-c7008297-6dfd-4a61-95c9-f90d09954e34.png__;!!Mih3wA!HTsMqkm9zjlXUo51sfx_NjGw5y4B8HeTBmbJAOtXCGqmQ-0pNy5J2-SQwsMAqWSTm_F4--vPta_62AvKVbfeUoGYgenRuA$

(I actually see the outline of the raster extent with values, but weirdly the screenshot doesn't work here.) QGIS

[image: image] https://urldefense.com/v3/__https://user-images.githubusercontent.com/2837257/235523967-e351378d-e351-4e4d-ba2b-9ade324ee8f4.png__;!!Mih3wA!HTsMqkm9zjlXUo51sfx_NjGw5y4B8HeTBmbJAOtXCGqmQ-0pNy5J2-SQwsMAqWSTm_F4--vPta_62AvKVbfeUoH5fuVAlQ$ R

library(terra) r <- rast("/Users/bbest/Downloads/idw_ffefc04c.tif") plot(r)

[image: image] https://urldefense.com/v3/__https://user-images.githubusercontent.com/2837257/235524503-6dd0002a-f977-4810-a0b4-e32440aff5ab.png__;!!Mih3wA!HTsMqkm9zjlXUo51sfx_NjGw5y4B8HeTBmbJAOtXCGqmQ-0pNy5J2-SQwsMAqWSTm_F4--vPta_62AvKVbfeUoHzkyGInQ$

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--

Erin Satterthwaite | she/her
Marine Ecologist & Sustainability Researcher
CalCOFI Program Coordinator
UC San Diego - Scripps Institution of Oceanography
California Sea Grant & CalCOFI
9500 Gilman Dr., La Jolla, CA 92093-0232
*work: *(858) 333-7265

*Play is the highest form of research *
                                 *   ~Albert Einstein*

[bbest]

The map points was giving me the error. Is there a way to have an image output that can work in mac preview?

Hi @evsatt, here's a couple quick updates:

• Fixed download points (*.csv) now works. (I forgot to load the readr library for write_csv() to work.)
• Added download image (*.png). It will generate a screenshot of the map (without the zoom and layer controls), and for the extent and zoom level of the current map view, like so:

[bbest]

Also @evsatt,

• I renamed Map links:
  • From: Download: [image (.png)]() , [points (.csv)](), [raster (.tif)](), [polygons (.geojson)]()
  • To: Download: [image.png]() , [points.csv]() , [raster.tif]() , [polygons.geojson]()
• And added [image.png]() to: Time series and Depth profile tabs.

[evsatt]

This is awesome! Thank you!

On Thu, May 4, 2023 at 5:39 AM Ben Best @.***> wrote:

Also @evsatt https://urldefense.com/v3/__https://github.com/evsatt__;!!Mih3wA!AcdgYguyRIvCscVEBq8gMtRO1EJl-Z9wHk-UA4pHXUjWev-2qNUejbCRQaZMAvn1yBwWXOmlDUweE8_HyeranTXrmqhbtg$ ,

• I renamed Map links:
  • From: Download: image (.png) , points (.csv), raster (.tif), polygons (.geojson)
  • To: Download: image.png , points.csv , raster.tif , polygons.geojson
• And added image.png to: Time series and Depth profile tabs.

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/CalCOFI/apps/issues/10*issuecomment-1534706093__;Iw!!Mih3wA!AcdgYguyRIvCscVEBq8gMtRO1EJl-Z9wHk-UA4pHXUjWev-2qNUejbCRQaZMAvn1yBwWXOmlDUweE8_HyeranTXREvd6rg$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AD356WLLODC3NWYUKN36BDDXEOPODANCNFSM6AAAAAAXSC5AZE__;!!Mih3wA!AcdgYguyRIvCscVEBq8gMtRO1EJl-Z9wHk-UA4pHXUjWev-2qNUejbCRQaZMAvn1yBwWXOmlDUweE8_HyeranTVqOUV-TQ$ . You are receiving this because you were mentioned.Message ID: @.***>

--

Erin Satterthwaite | she/her
Marine Ecologist & Sustainability Researcher
CalCOFI Program Coordinator
UC San Diego - Scripps Institution of Oceanography
California Sea Grant & CalCOFI
9500 Gilman Dr., La Jolla, CA 92093-0232
*work: *(858) 333-7265

*Play is the highest form of research *
                                 *   ~Albert Einstein*

[bbest]

Do have one little notification going, a la progress bar mention above, when selecting no data given space/time:

[bbest]

Jenn: would like to see matching color between Map and Table, eg Yellow/Yellow not Yellow/Blue.

[bbest]

Jenn: What does the Custom color mean, here blue from previous Existing:

[bbest]

Can we have consistent Area of Interest color cuing throughout, eg RED:

[bbest]

Jenn: can we have the CalCOFI grid centroids as "generalized station locations" (eg from calcofi4r) as a reference?

[bbest]

[bbest]

Endless loop with reactivity:

[bbest]

Darn sliver with Standard Nearshore:

[bbest]

Add headers, like "Sequential" and "Climatological" to the Time Series drop down; plus HelpText to explain difference.

• From API: time step over which to summarize; one of: a sequential increment ("decade", "year", "year.quarter", "year.month", "year.week", "date") or a climatology ("quarter","month","week","julianday","hour"). default is "year".

Only want options available based on data frequency.

• Could add another tab for Climatology and change plotting type to Box Plot, eg Quarters as factors.

• Perhaps only year and year-quarter are relevant when averaging over large areas.

[evsatt]

A few other follow ups from today: 1) [image: image.png] So it appears that in the time series maybe the seasons are being marked as (2016.1, 2016.2, 2016.3, 2016.4) -- so thats why there is a big break in this.

2) Can we fix the bin # -- the selection doesn't seem to work anyway...

[image: image.png] [image: image.png]

On Thu, May 11, 2023 at 11:43 AM Ben Best @.***> wrote:

Add headers, like "Sequential" and "Climatological" to the Time Series drop down; plus HelpText to explain difference.

[image: image] https://urldefense.com/v3/__https://user-images.githubusercontent.com/2837257/237783501-8b9efd3c-fd4e-4080-bc63-2f7da28baed7.png__;!!Mih3wA!BZduyf-HSpsHTZMYumk84oCv2yHjVwJc_hkT7PAdwm9GpxoJtXDxTuverSwz7b32JyFSKxQ9oTMzhgDf7asDE1K735AczA$

• From API https://urldefense.com/v3/__https://api.calcofi.io/__docs__/*/default/get_timeseries__;Iw!!Mih3wA!BZduyf-HSpsHTZMYumk84oCv2yHjVwJc_hkT7PAdwm9GpxoJtXDxTuverSwz7b32JyFSKxQ9oTMzhgDf7asDE1I7ptXtaw$: time step over which to summarize; one of: a sequential increment ("decade", "year", "year.quarter", "year.month", "year.week", "date") or a climatology ("quarter","month","week","julianday","hour"). default is "year".

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/CalCOFI/apps/issues/10*issuecomment-1544504905__;Iw!!Mih3wA!BZduyf-HSpsHTZMYumk84oCv2yHjVwJc_hkT7PAdwm9GpxoJtXDxTuverSwz7b32JyFSKxQ9oTMzhgDf7asDE1IuYNE9bA$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AD356WIHRMIO4QOO52AJNVDXFUXNNANCNFSM6AAAAAAXSC5AZE__;!!Mih3wA!BZduyf-HSpsHTZMYumk84oCv2yHjVwJc_hkT7PAdwm9GpxoJtXDxTuverSwz7b32JyFSKxQ9oTMzhgDf7asDE1KssBVOyQ$ . You are receiving this because you were mentioned.Message ID: @.***>

--

Erin Satterthwaite | she/her
Marine Ecologist & Sustainability Researcher
CalCOFI Program Coordinator
UC San Diego - Scripps Institution of Oceanography
California Sea Grant & CalCOFI
9500 Gilman Dr., La Jolla, CA 92093-0232
*work: *(858) 333-7265

*Play is the highest form of research *
                                 *   ~Albert Einstein*