Merge pull request #455 from stitam/resources

Expand ChEMBL resources and standardize webservice output

Author: stitam

.github/workflows/check-pkgdown.yml

@@ -1,3 +1,5 @@
+# based on https://docs.ropensci.org/rotemplate/
+
 on:
     push:
       branches:
@@ -9,25 +11,7 @@ on:
 name: check-pkgdown
 
 jobs:
-    check_pkgdown:
-      runs-on: ubuntu-22.04
-
-      env:
-        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-      steps:
-        - uses: actions/checkout@v4
-        - uses: r-lib/actions/setup-r@v2
-          with:
-            r-version: 'release'
-        - uses: r-lib/actions/setup-r-dependencies@v2
-          with:
-            extra-packages: any::devtools, any::pkgdown
-
-        - name: Install dependencies
-          run: devtools::install_github("https://github.com/ropensci-org/rotemplate")
-          shell: Rscript {0}
-
-        - name: Check pkgdown
-          run: pkgdown::check_pkgdown()
-          shell: Rscript {0}
+  check_pkgdown:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: ropensci-org/rotemplate@main

DESCRIPTION

@@ -47,6 +47,7 @@ Imports:
     rlang,
     utils
 Suggests:
+    dbplyr (>= 2.2.1),
     testthat,
     rcdk,
     covr,

NEWS.md

@@ -4,7 +4,8 @@
 
 ### OFFLINE ACCESS
 
-* `chembl_query()` can now perform both online queries (`mode = "ws"`, default) and offline retrievals (`mode = "offline"`) from a local ChEMBL database. Offline mode currently supports the following resources: `atc_class`, `binding_site`, `biotherapeutic`, `cell_line`, `chembl_id_lookup`, `compound_record`, and `document`.
+* `chembl_query()` can now perform both online queries (`mode = "ws"`, default) and offline retrievals (`mode = "offline"`) from a local ChEMBL database. Offline mode currently supports the following resources: `assay`, `atc_class`, `binding_site`, `biotherapeutic`, `cell_line`, `chembl_id_lookup`, `compound_record`, `document`, `drug_indication`, `drug_warning`, `go_slim`.
+* Results for online and offline queries are identical for most resources. If there are differences, the offline version throws informative warnings.
 * Added a new function `db_download_chembl()` for downloading ChEMBL for fully offline access.
 
 ### OTHER
@@ -17,7 +18,7 @@
 
 ## MINOR IMPROVEMENTS
 
-* `chembl_query()` now returns a named list with improved formatting for nested output.
+* `chembl_query()` now returns a named list with improved formatting for nested output when `output = "tidy"`.
 * Added new argument `output` to `chembl_query()` (values: "raw" or "tidy") to control output format. Raw format returns the full nested structure; tidy format attempts to flatten the results.
 * Added new `options` argument to `chembl_query()` for passing resource- and mode-specific options (cache file name, similarity threshold, database version, etc.).
 * `chembl_query()` can now replace NULL values with typed NA values (`NA_character_`, `NA_integer_`, `NA_real_`) based on the field schema when `replace_nulls = TRUE` in options. For this, the schema is retrieved from ChEMBL and cached for the session.