fix: verify the metadata database certificate with sslmode=verify-full (#235)

Part of https://codefloe.com/rpkgs/bincraft/issues/225. Stacked on #234.

Every connection to the metadata database used `sslmode = 'require'`, which encrypts but does not authenticate the server, so anyone able to impersonate `r-binaries.devxy.io:15432` would receive `PGPASS`.

## Changes

- `.crow/build-all-versions.yaml`, `process-updates.yaml`, `prune-stale-flat-binaries.yaml`, `reindex.yaml`, `weekly-rebuild-reindex.yaml`: `metadata_db_sslmode = 'verify-full'` in every bincraft call.
- `local/*.R`: the same for bincraft calls; scripts that call `DBI::dbConnect()` directly also pass `sslrootcert = bincraft::postgres_sslrootcert("verify-full")`, because libpq looks for `~/.postgresql/root.crt` rather than the system trust store.
- `README.md`: note that the endpoint serves a Let's Encrypt certificate and how to verify it.
- air reformatted three `=` assignments to `<-` in `local/missing-cran-packages-db.R` and `local/packages-without-any-binary.R` while the hook ran on those files.

## Ordering: merge last

1. devxy/k8s-talos#417 must be live: today the server presents an in-cluster certificate from a private CA, which `verify-full` rejects.
2. https://codefloe.com/rpkgs/bincraft/pulls/226 must be released: `local/install-bincraft.R` installs the latest tag, and older releases neither pass a root certificate nor export `postgres_sslrootcert()`.
3. #234 must be merged.

Merging early fails every database connection in CI, and since #234 per-minor reindex failures fail the pipeline.

Reviewed-on: #235

local/backfill-abi-classification.R

@@ -47,7 +47,7 @@ db <- list(
   metadata_db_port = 15432L,
   metadata_db_user = "rpkgs",
   metadata_db_password = Sys.getenv("PGPASS"),
-  metadata_db_sslmode = "require"
+  metadata_db_sslmode = "verify-full"
 )
 
 read_index <- function(index_url) {

local/build-all.R

@@ -152,7 +152,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "rpkgs",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 # Scope the skip to the R minor this pass is running under. `single_builds`
 # records `r_version` per attempt, but querying without it made a non-primary
@@ -250,7 +251,7 @@ mapply(
       metadata_db_table = "single_builds",
       metadata_db_user = "rpkgs",
       metadata_db_password = Sys.getenv("PGPASS"),
-      metadata_db_sslmode = "require",
+      metadata_db_sslmode = "verify-full",
       metadata_db_port = 15432,
       archive = TRUE,
       patches = "local/patches",

local/build-newer-r.R

@@ -48,7 +48,7 @@ if ("--dry-run" %in% args) {
         metadata_db_name = "build_metadata",
         metadata_db_user = "rpkgs",
         metadata_db_password = Sys.getenv("PGPASS"),
-        metadata_db_sslmode = "require",
+        metadata_db_sslmode = "verify-full",
         metadata_db_port = 15432
       ),
       s3_endpoint = "https://s3.eu-central-003.backblazeb2.com",
@@ -61,7 +61,7 @@ if ("--dry-run" %in% args) {
       metadata_db_table = "single_builds",
       metadata_db_user = "rpkgs",
       metadata_db_password = Sys.getenv("PGPASS"),
-      metadata_db_sslmode = "require",
+      metadata_db_sslmode = "verify-full",
       metadata_db_port = 15432,
       archive = TRUE,
       patches = "local/patches",

local/build-one.R

@@ -115,7 +115,7 @@ for (ver in versions) {
     metadata_db_table = "single_builds",
     metadata_db_user = "rpkgs",
     metadata_db_password = Sys.getenv("PGPASS"),
-    metadata_db_sslmode = "require",
+    metadata_db_sslmode = "verify-full",
     metadata_db_port = 15432
   )
   if (sensitive) touched_minor <- TRUE else touched_generic <- TRUE

local/failing-builds-report.R

@@ -69,7 +69,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "rpkgs",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 on.exit(DBI::dbDisconnect(con), add = TRUE)
 

local/label-removed-cran-packages.R

@@ -13,7 +13,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "r_binaries",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 
 pkgs_db <- query_metadata_table() |>

local/list-unsafe-flat-objects.R

@@ -30,7 +30,8 @@ con <- DBI::dbConnect(
   port = 15432L,
   user = "rpkgs",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 on.exit(try(DBI::dbDisconnect(con), silent = TRUE), add = TRUE)
 

local/missing-cran-packages-db.R

@@ -10,7 +10,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "r_binaries",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 
 `%nin%` <- Negate(`%in%`)
@@ -45,12 +46,12 @@ data <- dbGetQuery(
   "SELECT name FROM single_builds WHERE platform = $1 AND arch = $2 and removed = FALSE;",
   params = list(platform, arch)
 )
-removed_pkgs = get_removed_cran_packages(lubridate::interval(
+removed_pkgs <- get_removed_cran_packages(lubridate::interval(
   lubridate::today(),
   lubridate::today() - 2
 ))$name
 pkgs_db <- unique(data$name)
-pkgs_db = setdiff(pkgs_db, removed_pkgs)
+pkgs_db <- setdiff(pkgs_db, removed_pkgs)
 
 pkgs <- setdiff(cran_pkgs, pkgs_db)
 formatted_pkgs <- gsub(

local/packages-to-build.R

@@ -32,7 +32,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "rpkgs",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 
 cran_archive <- tools::CRAN_archive_db()

local/packages-without-any-binary.R

@@ -8,7 +8,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "r_binaries",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 
 cran_pkgs <- tools::CRAN_package_db() |>
@@ -27,7 +28,7 @@ pkgs <- data |>
   distinct(name) |>
   pull(name)
 
-pkgs = setdiff(cran_pkgs, pkgs)
+pkgs <- setdiff(cran_pkgs, pkgs)
 # Format, remove line breaks, and print as a single line
 formatted_pkgs <- gsub(
   '"',

local/proposal-tracking.R

@@ -53,7 +53,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "rpkgs",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 on.exit(DBI::dbDisconnect(con), add = TRUE)
 

local/propose-patches.R

@@ -87,7 +87,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "rpkgs",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 on.exit(DBI::dbDisconnect(con), add = TRUE)
 

local/prune-stale-flat-binaries.R

@@ -86,7 +86,8 @@ if (length(explicit) > 0L) {
     port = 15432L,
     user = "rpkgs",
     password = Sys.getenv("PGPASS"),
-    sslmode = "require"
+    sslmode = "verify-full",
+    sslrootcert = bincraft::postgres_sslrootcert("verify-full")
   )
   on.exit(try(DBI::dbDisconnect(con), silent = TRUE), add = TRUE)
 

local/rebuild-missing.R

@@ -171,7 +171,7 @@ for (i in seq_along(mine)) {
       metadata_db_table = "single_builds",
       metadata_db_user = "rpkgs",
       metadata_db_password = Sys.getenv("PGPASS"),
-      metadata_db_sslmode = "require",
+      metadata_db_sslmode = "verify-full",
       metadata_db_port = 15432,
       archive = TRUE,
       upload = TRUE,

local/repair-built-stamp.R

@@ -172,7 +172,7 @@ for (minor in r_minors) {
         metadata_db_port = 15432L,
         metadata_db_user = "rpkgs",
         metadata_db_password = Sys.getenv("PGPASS"),
-        metadata_db_sslmode = "require"
+        metadata_db_sslmode = "verify-full"
       )
       TRUE
     },

local/weekly-missing-binaries-audit.R

@@ -60,7 +60,8 @@ con <- DBI::dbConnect(
   port = 15432,
   user = "rpkgs",
   password = Sys.getenv("PGPASS"),
-  sslmode = "require"
+  sslmode = "verify-full",
+  sslrootcert = bincraft::postgres_sslrootcert("verify-full")
 )
 
 errored_pkgs <- DBI::dbGetQuery(