Merge remote-tracking branch 'origin/main' into use-api

* origin/main: Add printing to remaining classes (#31) Improve error messages (#30) Update documentation (#29) Return `NULL` when a record's related field is empty (#28) minor fix in usage vignette (#32) Add usage vignette (#18) Add a simple unit test which queries laminlabs/lamindata (#27) bump action from v4.5.0 to v4 (#26)
laminlabs · Oct 14, 2024 · 6e3e7ae · 6e3e7ae
2 parents 5dd2611 + bca4137
commit 6e3e7ae
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -46,15 +46,15 @@ jobs:
 
       - name: Install lamindb
         run: |
-          pip install lamindb[bionty]
+          pip install lamindb[bionty,wetlab]
 
       - name: Log in to Lamin
         run: |
           lamin login
 
       - name: Set cellxgene as default instance
         run: |
-          lamin load laminlabs/cellxgene
+          lamin connect laminlabs/cellxgene
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -44,23 +44,23 @@ jobs:
 
       - name: Install lamindb
         run: |
-          pip install lamindb[bionty]
+          pip install lamindb[bionty,wetlab]
 
       - name: Log in to Lamin
         run: |
           lamin login
 
       - name: Set cellxgene as default instance
         run: |
-          lamin load laminlabs/cellxgene
+          lamin connect laminlabs/cellxgene
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: false
           branch: gh-pages

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,9 +6,9 @@
 
 * Read user settings from env file created by lamin Python package (PR #2, PR #8).
 
-* Render a pkgdown website (PR #13).
+* Add `to_string()` and `print()` methods to the `Record` class and (incomplete) `describe()` method to the `Artifact()` class (PR #22).
 
-* Add `to_string()` and `print()` methods to the `Record` class and (incomplete) `describe()` method to the `Artifact()` class (PR #22)
+* Add `to_string()` and `print()` methods to remaining classes (PR #31)
 
 ## MAJOR CHANGES
 
@@ -19,26 +19,44 @@
   - Linting action.
   - Commands for roxygenizing (`/document`) and restyling the source code (`/style`).
 
-* Allow unauthenticated users to connect to an instance if they ran `lamin load <instance>` beforehand (PR #19).
+* Allow unauthenticated users to connect to an instance if they ran `lamin connect <instance>` beforehand (PR #19).
 
 ## MINOR CHANGES
 
-* Update `README` with new set up instructions and simplify (PR #14).
-
 * Do not complain when foreign keys are not found in a record, but also do not complain when they are (PR #13).
 
-* Further simplify the `README`, and move the detailed usage description to a separate vignette (PR #13).
+* Define a current user and current instance with lamin-cli prior to testing and generating documentation in the CI (PR #23).
+
+## TESTING
+
+* Add a simple unit test which queries laminlabs/lamindata (PR #27).
+
+* Added unit test for the InstanceAPI class (PR #30).
+
+## DOCUMENTATION
+
+* Update `README` with new set up instructions and simplify (PR #14).
 
 * Add a `pkgdown` website to the project (PR #13).
 
+* Further simplify the `README`, and move the detailed usage description to a separate vignette (PR #13).
+
 * Generate vignettes using Quarto (PR #13).
 
-* Define a current user and current instance with lamin-cli prior to testing and generating documentation in the CI (PR #23).
+* Add vignette to showcase laminr usage (PR #18).
+
+* Replace all mentions of `lamin load` with `lamin connect` (PR #29).
+
+* Improve the `README` (PR #29).
 
 ## BUG FIXES
 
 * Fixed the parsing of the env files in `~/.lamin` due to changes in the lamindb-setup Python package (PR #12).
 
+* Return `NULL` when a record's related field is empty (PR #28).
+
+* Add alternative error message when no message is returned from the API (PR #30).
+
 # laminr v0.0.1
 
 Initial POC implementation of the LaminDB API client for R.

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,5 +26,8 @@ Imports:
 Suggests:
     anndata,
     quarto,
-    s3 (>= 1.1.0)
+    s3 (>= 1.1.0),
+    testthat (>= 3.0.0),
+    withr
 VignetteBuilder: quarto
+Config/testthat/edition: 3
diff --git a/R/Artifact.R b/R/Artifact.R
@@ -8,10 +8,9 @@ ArtifactRecord <- R6::R6Class( # nolint object_name_linter
   "ArtifactRecord",
   inherit = Record,
   public = list(
-    #' Load the artifact into memory
-    #'
     #' @description
-    #' This currently only supports AnnData artifacts.
+    #' Load the artifact into memory. This currently only supports AnnData
+    #' artifacts.
     #'
     #' @return The artifact
     load = function() {
@@ -26,10 +25,9 @@ ArtifactRecord <- R6::R6Class( # nolint object_name_linter
         cli_abort(paste0("Unsupported accessor: ", artifact_accessor))
       }
     },
-    #' Cache the artifact to the local filesystem
-    #'
     #' @description
-    #' This currently only supports S3 storage.
+    #' Cache the artifact to the local filesystem. This currently only supports
+    #' S3 storage.
     #'
     #' @return The path to the cached artifact
     cache = function() {
@@ -50,6 +48,10 @@ ArtifactRecord <- R6::R6Class( # nolint object_name_linter
         cli_abort(paste0("Unsupported storage type: ", artifact_storage$type))
       }
     },
+    #' @description
+    #' Print a more detailed description of an `ArtifactRecord`
+    #'
+    #' @param style Logical, whether the output is styled using ANSI codes
     describe = function(style = TRUE) {
       provenance_fields <- c(
         storage = "root",

diff --git a/R/Field.R b/R/Field.R
@@ -45,6 +45,39 @@ Field <- R6::R6Class( # nolint object_name_linter
       private$.related_field_name <- related_field_name
       private$.related_registry_name <- related_registry_name
       private$.related_module_name <- related_module_name
+    },
+    #' @description
+    #' Print a `Field`
+    #'
+    #' @param style Logical, whether the output is styled using ANSI codes
+    print = function(style = TRUE) {
+      cli::cat_line(self$to_string(style))
+    },
+    #' @description
+    #' Create a string representation of a `Field`
+    #'
+    #' @param style Logical, whether the output is styled using ANSI codes
+    #'
+    #' @return A `cli::cli_ansi_string` if `style = TRUE` or a character vector
+    to_string = function(style = FALSE) {
+      field_strings <- make_key_value_strings(
+        self,
+        c(
+          "field_name",
+          "column_name",
+          "type",
+          "registry_name",
+          "module_name",
+          "through",
+          "is_link_table",
+          "relation_type",
+          "related_field_name",
+          "related_registry_name",
+          "related_module_name"
+        )
+      )
+
+      make_class_string("Field", field_strings, style = style)
     }
   ),
   private = list(

diff --git a/R/Instance.R b/R/Instance.R
@@ -104,6 +104,114 @@ Instance <- R6::R6Class( # nolint object_name_linter
     #' Get the names of the modules. Example: `c("core", "bionty")`.
     get_module_names = function() {
       names(private$.module_classes)
+    },
+    #' Get instance settings.
+    get_settings = function() {
+      private$.settings
+    },
+    #' Get instance API.
+    get_api = function() {
+      private$.api
+    },
+    #' @description
+    #' Print an `Instance`
+    #'
+    #' @param style Logical, whether the output is styled using ANSI codes
+    print = function(style = TRUE) {
+
+      registries <- self$get_module("core")$get_registries()
+
+      is_link_table <- purrr::map(registries, "is_link_table") |>
+        unlist()
+
+      standard_lines <- purrr::map_chr(
+        names(registries)[!is_link_table],
+        function(.registry) {
+          cli::col_blue(paste0("    $", registries[[.registry]]$class_name))
+        }
+      )
+
+      link_lines <- purrr::map_chr(
+        names(registries)[is_link_table],
+        function(.registry) {
+          cli::col_blue(paste0("    ", .registry))
+        }
+      )
+
+      lines <- c(
+        cli::style_bold(cli::col_green(private$.settings$name)),
+        cli::style_italic(cli::col_magenta("  Core registries")),
+        standard_lines,
+        cli::style_italic(cli::col_magenta("  Core link tables")),
+        link_lines
+      )
+
+      module_names <- self$get_module_names()
+      module_names <- module_names[module_names != "core"]
+
+      if (length(module_names) > 0) {
+        lines <- c(
+          lines,
+          cli::style_italic(cli::col_magenta("  Additional modules")),
+          cli::col_blue(paste0("    ", module_names))
+        )
+      }
+
+      if (isFALSE(style)) {
+        lines <- cli::ansi_strip(lines)
+      }
+
+      purrr::walk(lines, cli::cat_line)
+    },
+    #' @description
+    #' Create a string representation of an `Instance`
+    #'
+    #' @param style Logical, whether the output is styled using ANSI codes
+    #'
+    #' @return A `cli::cli_ansi_string` if `style = TRUE` or a character vector
+    to_string = function(style = FALSE) {
+      registries <- self$get_module("core")$get_registries()
+
+      is_link_table <- purrr::map(registries, "is_link_table") |>
+        unlist()
+
+      mapping <- list(
+        "CoreRegistries" = paste0(
+          "[",
+          paste(
+            paste0(
+              "$",
+              purrr::map_chr(registries[!is_link_table], "class_name")
+            ),
+            collapse = ", "
+          ),
+          "]"
+        ),
+        "CoreLinkTables" = paste0(
+          "[",
+          paste(names(registries[is_link_table]), collapse = ", "),
+          "]"
+        )
+      )
+
+      module_names <- self$get_module_names()
+      module_names <- module_names[module_names != "core"]
+
+      if (length(module_names) > 0) {
+        mapping["AdditionalModules"] <- paste0(
+          "[",
+          paste(module_names, collapse = ", "),
+          "]"
+        )
+      }
+
+      key_value_strings <- make_key_value_strings(
+        mapping, quote_strings = FALSE
+      )
+
+      make_class_string(
+        private$.settings$name, key_value_strings, style = style
+      )
     }
   ),
   private = list(

diff --git a/R/InstanceAPI.R b/R/InstanceAPI.R
@@ -18,6 +18,7 @@ InstanceAPI <- R6::R6Class( # nolint object_name_linter
       private$.api_client <- laminr.api::ApiClient$new(instance_settings$api_url)
       private$.default_api <- laminr.api::DefaultApi$new(private$.api_client)
     },
+    #' @description
     #' Get the schema for the instance.
     get_schema = function(id) {
       schema <- try(
@@ -35,7 +36,9 @@ InstanceAPI <- R6::R6Class( # nolint object_name_linter
 
       return(schema)
     },
+    #' @description
     #' Get a record from the instance.
+    #'
     #' @importFrom jsonlite toJSON
     get_record = function(module_name,
                           registry_name,
@@ -87,12 +90,42 @@ InstanceAPI <- R6::R6Class( # nolint object_name_linter
         ))
       }
 
-      return(record)
+      content
     }
   ),
   private = list(
     .instance_settings = NULL,
-    .api_client = NULL,
-    .default_api = NULL
+    process_response = function(response, request_type) {
+      content <- httr::content(response)
+      if (httr::http_error(response)) {
+        if (is.list(content) && "detail" %in% names(content)) {
+          cli_abort(content$detail)
+        } else {
+          cli_abort("Failed to {request_type} from instance. Output: {content}")
+        }
+      }
+
+      content
+    },
+    #' @description
+    #' Print an `API`
+    #'
+    #' @param style Logical, whether the output is styled using ANSI codes
+    print = function(style = TRUE) {
+      cli::cat_line(self$to_string(style))
+    },
+    #' @description
+    #' Create a string representation of an `API`
+    #'
+    #' @param style Logical, whether the output is styled using ANSI codes
+    #'
+    #' @return A `cli::cli_ansi_string` if `style = TRUE` or a character vector
+    to_string = function(style = FALSE) {
+      field_strings <- make_key_value_strings(
+        private$.instance_settings, c("api_url", "id", "schema_id")
+      )
+
+      make_class_string("API", field_strings, style = style)
+    }
   )
 )