fold rest of content into output report

bbest commented 2 years ago

Here's the content that is queryable in the app and folded into the output custom report:

[x] Projects
[x] Management
[x] Documents
[x] Publications
[x] Spatial

bbest commented 2 years ago

Working off apps_dev branch in /share/github/apps_dev displayed in:

shiny.marineenergy.app/report-v2-dev

per:

ls -la  /srv/shiny-server
report-v2-dev -> /share/github/apps_dev/report-v2

bbest commented 2 years ago

app: report-v2

Purpose: configure the API request to generate the report.

Working off apps_dev branch in /share/github/apps_dev displayed in:

shiny.marineenergy.app/report-v2-dev

per:

ls -la  /srv/shiny-server
report-v2-dev -> /share/github/apps_dev/report-v2

ui.R: btn_rpt_create: https://github.com/marineenergy/apps/blob/51380df264f05d73a7a5b3acaf5f0b18a7d4a2b6/report-v2/ui.R#L273
server.R: input$btn_rpt_create: https://github.com/marineenergy/apps/blob/51380df264f05d73a7a5b3acaf5f0b18a7d4a2b6/report-v2/server.R#L717-L772
Submits to the api url_rpt_pfx "https://api.marineenergy.app/report", which is the report endpoint of the https://api.marineenergy.app.

api: generate the report

run-api.R#L5

plumber_r <- "/share/github/api/plumber.R"

plumber.R#L91-L154

# TODO: reset default values to Null or blank
function(
  req,
  email        = "bdbest@gmail.com",
  date         = "2021-05-25 19:11:49 UTC",
  title        = "Test Report",
  filetype     = "html",
  contents     = '{"Projects":[true],"Management":[true]}',
  interactions = '[["Receptor.Fish","Stressor.PhysicalInteraction.Collision"],["Technology.Wave","Receptor.Birds"]]',
  res) {
...
dir_rpt_pfx <- "/share/user_reports"
...
r_script    <- "/share/github/api/scripts/render_yml.R"
...
# get hash for unique filename by digesting metadata
hsh <- digest::digest(m, algo="crc32")
yml <- glue::glue("{dir_rpt_pfx}/{email}/report_{hsh}.yml")
...
cmd <- glue::glue('r_script={r_script}\n yml={yml}\n log={log}\n $r_script $yml > $log 2>> $log')
...
system(cmd, wait = F)

render_yml.R#L8-L73

setwd("/share/github/api")
template_rmd <- "/share/github/api/_report.Rmd"
source("/share/github/apps_dev/scripts/common.R")
source(file.path(dir_scripts, "report.R"))
...
# write Rmd of custom report
message("frontmatter for Rmd... ----")
message(yaml::as.yaml(fm))
...
message("rendering...")
rmarkdown::render(
  input         = rmd,
  output_file   = out)

bbest commented 2 years ago

Let's look at example reports in /share/user_reports/ben@ecoquants.com that currently:

do render Test w/ Cristina: marmam & noise | 2021-11-10 21:44:22 UTC | Published | Projects, Management | 1 report_81fb65d5.yml:

email: ben@ecoquants.com
date: 2021-11-10 21:44:22 UTC
title: 'Test w/ Cristina: marmam & noise'
filetype: html
contents:
  projects: yes
  management: yes
interactions:
- - Receptor.MarineMammals
  - Stressor.Noise

do NOT render Testing w/ Tech Crew | 2021-11-09 21:57:56 UTC | Rendering... | Projects, Management | 0 report_b7388e28.yml

email: ben@ecoquants.com
date: 2021-11-09 21:57:56 UTC
title: Testing w/ Tech Crew
filetype: html
contents:
  projects: yes
  management: yes
interactions: []

bbest commented 2 years ago

PROBLEM: Need tabular output for content without any interactions provided

The report API is only setup to write outputs per content type given a set of interactions (ie combinations of technology/stressor/receptor tags).

This is handled in render_yml.R#L64 with the rpt_content() function:

  r <- lapply(contents, rpt_content, ixns = p$interactions, rmd = rmd)

And this function is defined in:

https://github.com/marineenergy/apps/blob/51380df264f05d73a7a5b3acaf5f0b18a7d4a2b6/scripts/report.R#L14-L57

So need to make another option, like in render_yml.R#L64:

if (length(p$interactions) == 0) { 
  # TODO: return table of all content 
} else {
  # carry on as originally designed
  r <- lapply(contents, rpt_content, ixns = p$interactions, rmd = rmd)
}`

marineenergy / apps