EPIC: Plot refactor metadata

.github/workflows/R-CMD-check.yaml

@@ -18,6 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -34,6 +35,12 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libssh-dev
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
@@ -47,10 +54,16 @@ jobs:
           needs: check
 
       - name: Start Redis
+        if: runner.os != 'Windows'
         uses: shogo82148/actions-setup-redis@v1
         with:
           redis-version: "5.x"
 
+      - name: Start Redis (windows)
+        if: runner.os == 'Windows'
+        run: |
+          choco install memurai-developer
+
       - name: Build test data
         run: Rscript ./scripts/build_test_data
 

.github/workflows/R-integration-test.yaml

@@ -18,6 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -32,6 +33,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libssh-dev
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -46,10 +53,15 @@ jobs:
           extra-packages: any::devtools
 
       - name: Start Redis
+        if: runner.os != 'Windows'
         uses: shogo82148/actions-setup-redis@v1
         with:
           redis-version: "5.x"
 
+      - name: Start Redis (windows)
+        if: runner.os == 'Windows'
+        run: |
+          choco install memurai-developer
       - name: Build test data
         run: |
           ./scripts/build_test_data

.github/workflows/docker.yaml

@@ -9,8 +9,8 @@ on:
 env:
   TAG_SERVER_DH: mrcide/hintr
   TAG_WORKER_DH: mrcide/hintr-worker
-  TAG_SERVER_GHCR: mrc-ide/hintr
-  TAG_WORKER_GHCR: mrc-ide/hintr-worker
+  TAG_SERVER_GHCR: hivtools/hintr
+  TAG_WORKER_GHCR: hivtools/hintr-worker
 
 jobs:
   docker:
@@ -32,6 +32,9 @@ jobs:
           fi
           echo "CI_SHA=${LONG_SHA:0:7}" >> $GITHUB_OUTPUT
 
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 

.github/workflows/pkgdown.yaml

@@ -24,6 +24,12 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libssh-dev
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

.github/workflows/test-coverage.yaml

@@ -17,6 +17,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libssh-dev
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
@@ -28,10 +34,16 @@ jobs:
           needs: coverage
 
       - name: Start Redis
+        if: runner.os != 'Windows'
         uses: shogo82148/actions-setup-redis@v1
         with:
           redis-version: "5.x"
 
+      - name: Start Redis (windows)
+        if: runner.os == 'Windows'
+        run: |
+          choco install memurai-developer
+
       - name: Build test data
         run: |
           ./scripts/build_test_data

.lintr

@@ -1,7 +1,6 @@
-linters: with_defaults(
+linters: linters_with_defaults(
     object_length_linter = NULL,
     object_name_linter = NULL,
     object_usage_linter = NULL,
-    cyclocomp_linter = NULL
-    )
+    cyclocomp_linter = NULL)
 exclusions: list("tests/testthat.R")

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hintr
 Title: R API for calling naomi district level HIV model
-Version: 1.1.26
+Version: 1.2.0
 Authors@R: 
     person(given = "Robert",
            family = "Ashton",
@@ -23,7 +23,7 @@ Imports:
     glue,
     ids,
     jsonlite (>= 1.2.2),
-    naomi (>= 2.9.24),
+    naomi (>= 2.9.27),
     naomi.options (>= 1.1.0),
     porcelain (>= 0.1.8),
     qs,
@@ -40,6 +40,7 @@ Suggests:
     callr,
     cli,
     covr,
+    duckdb,
     httr,
     jsonvalidate,
     mockery,

NEWS.md

@@ -1,3 +1,9 @@
+# hintr 1.2.0
+
+* Update plot metadata format to make it more generic and generally usable
+* Add a new endpoint `/review-input/metadata` to return metadata for all input plots
+* Remove `/meta/plotting` and `/meta/plotting<iso3>` endpoints as these are no longer used
+
 # hintr 1.1.16
 
 * Add an optional arg to API startup to turn on a health-check. If set, the interval after which the next time the redis connection is used the connection will be reset. 0 for no reconnection. This is needed for running on cloud services as they close idle tcp connections after a set time. On Azure it if 4 mins, so we need to the client to be able to reconnect if this interval has passed.

R/api.R

@@ -5,6 +5,7 @@ api_build <- function(queue, validate = FALSE, logger = NULL) {
   api$handle(endpoint_baseline_combined())
   api$handle(endpoint_validate_survey_programme())
   api$handle(endpoint_input_time_series_plot())
+  api$handle(endpoint_review_input_metadata())
   api$handle(endpoint_model_options())
   api$handle(endpoint_model_options_validate())
   api$handle(endpoint_model_submit(queue))
@@ -15,14 +16,11 @@ api_build <- function(queue, validate = FALSE, logger = NULL) {
   api$handle(endpoint_model_calibrate_options())
   api$handle(endpoint_model_calibrate_submit(queue))
   api$handle(endpoint_model_calibrate_status(queue))
-  api$handle(endpoint_model_calibrate_result(queue))
   api$handle(endpoint_model_calibrate_metadata(queue))
   api$handle(endpoint_model_calibrate_data(queue))
   api$handle(endpoint_model_calibrate_result_path(queue))
   api$handle(endpoint_model_calibrate_plot(queue))
   api$handle(endpoint_comparison_plot(queue))
-  api$handle(endpoint_plotting_metadata_iso3())
-  api$handle(endpoint_plotting_metadata_default())
   api$handle(endpoint_download_submit(queue))
   api$handle(endpoint_download_status(queue))
   api$handle(endpoint_download_result(queue))
@@ -183,6 +181,18 @@ endpoint_input_time_series_plot <- function() {
                                     returning = response)
 }
 
+endpoint_review_input_metadata <- function() {
+  input <- porcelain::porcelain_input_body_json(
+    "input", "ReviewInputFilterMetadataRequest.schema", schema_root())
+  response <- porcelain::porcelain_returning_json(
+    "ReviewInputFilterMetadataResponse.schema", schema_root())
+  porcelain::porcelain_endpoint$new("POST",
+                                    "/review-input/metadata",
+                                    review_input_filter_metadata,
+                                    input,
+                                    returning = response)
+}
+
 returning_json_version <- function(schema = NULL, root = NULL,
                                    status_code = 200L) {
   ## This is the same as porcelain::porcelain_returning_json except we
@@ -358,23 +368,6 @@ endpoint_comparison_plot <- function(queue) {
                                     returning = response)
 }
 
-endpoint_plotting_metadata_iso3 <- function() {
-  endpoint_plotting_metadata("/meta/plotting/<iso3>")
-}
-
-endpoint_plotting_metadata_default <- function() {
-  endpoint_plotting_metadata("/meta/plotting")
-}
-
-endpoint_plotting_metadata <- function(path) {
-  response <- porcelain::porcelain_returning_json(
-    "PlottingMetadataResponse.schema", schema_root())
-  porcelain::porcelain_endpoint$new("GET",
-                                    path,
-                                    plotting_metadata,
-                                    returning = response)
-}
-
 ## Return same headers as binary returning but ensure no body is returned.
 returning_binary_head <- function(status_code = 200L) {
   porcelain::porcelain_returning("application/octet-stream",

R/calibrate.R

@@ -10,7 +10,7 @@ run_calibrate <- function(model_output, calibration_options, path_results,
     })
   }
 
-  path_results <- normalizePath(path_results, mustWork = TRUE)
+  path_results <- normalizePath(path_results, winslash = "/", mustWork = TRUE)
   plot_data_path <- tempfile("plot_data", tmpdir = path_results,
                              fileext = ".duckdb")
   model_output_path <- tempfile("model_output", tmpdir = path_results,

R/downloads.R

@@ -17,7 +17,7 @@ download <- function(model_output, type, path_results, input, language = NULL) {
                      agyw = ".xlsx",
                      hintr_error(t_("INVALID_DOWNLOAD_TYPE", list(type = type)),
                                  "INVALID_DOWNLOAD_TYPE"))
-  path_results <- normalizePath(path_results, mustWork = TRUE)
+  path_results <- normalizePath(path_results, winslash = "/", mustWork = TRUE)
   download_path <- tempfile(type, tmpdir = path_results, fileext = file_ext)
 
   if (type == "spectrum") {