v0.3.0

.github/workflows/pkgdown.yml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - dev
+      - master
+
+name: Deploy-package-documentation
+
+jobs:
+  pkgdown:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package documentation
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, commit_message="deploy docs with a github action")'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BiocProject
 Title: Bioconductor Management with Portable Encapsulated Project (PEP) Objects
-Version: 0.2.1
+Version: 0.3.0
 Authors@R: c(person("Michal", "Stolarczyk", email = "mjs5kd@virginia.edu",role = c("aut", "cre")), 
 	person("Nathan", "Sheffield", email = "nathan@code.databio.org",role = c("aut")))
 Description: A Bioconductor-oriented project management class. It wraps the
@@ -9,8 +9,9 @@ Description: A Bioconductor-oriented project management class. It wraps the
 License: BSD_2_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Depends: S4Vectors, pepr, methods
-Suggests: testthat, yaml, BiocFileCache, simpleCache, GenomicRanges, knitr, BiocStyle, rmarkdown
+Depends: S4Vectors, pepr
+Imports: methods, glue, RCurl, yaml, stats, pryr
+Suggests: testthat, BiocFileCache, simpleCache, GenomicRanges, knitr, BiocStyle, rmarkdown
 biocViews: DataImport, DataRepresentation
 RoxygenNote: 7.1.1
 URL: https://github.com/pepkit/BiocProject

NAMESPACE

@@ -1,13 +1,27 @@
 # Generated by roxygen2: do not edit by hand
 
 export(.insertPEP)
+export(.pyToR)
 export(.setShowMethod)
 export(.unionList)
 export(BiocProject)
+export(gatherPipelineInterfaces)
+export(getOutputsBySample)
+export(getProjectOutputs)
+export(pipelineInterfacesBySample)
+export(readSchema)
 exportMethods(config)
 exportMethods(getProject)
 exportMethods(is)
 exportMethods(sampleTable)
 import(S4Vectors)
 import(methods)
 import(pepr)
+importFrom(RCurl,getURLContent)
+importFrom(glue,glue)
+importFrom(methods,new)
+importFrom(pepr,checkSection)
+importFrom(pepr,config)
+importFrom(pryr,partial)
+importFrom(stats,setNames)
+importFrom(yaml,yaml.load_file)

R/constants.R

@@ -7,4 +7,15 @@
 BIOC_SECTION = "bioconductor"
 FUNCTION_ARGS = "funcArgs"
 FUNCTION_PATH = "readFunPath"
-FUNCTION_NAME = "readFunName"
+FUNCTION_NAME = "readFunName"
+
+# other constants
+PIP_TYPE_KEY = "pipeline_type"
+PIP_NAME_KEY = "pipeline_name"
+OUTPUT_SCHEMA_SECTION = "output_schema"
+LOOPER_SECTION = "looper"
+PIP_IFACE_NAME = "pipeline_interfaces"
+PIP_IFACE_KEY = "pipeline_interfaces_key"
+SCHEMA_SAMPLE_OUTS = c("properties", "samples", "items", "properties")
+PATH_LIKE_KEYS = c("path", "thumbnail_path")
+PIP_IFACE_SECTION = c(LOOPER_SECTION, PIP_IFACE_NAME)

R/functions.R

@@ -63,6 +63,8 @@
 #'  the \code{bioconductor} section in the config file.
 #' @param autoLoad a logical indicating whether the data should be loaded
 #'  automatically. See \code{Details} for more information.
+#' @param projectLevel logical indicating whether a only project-level pifaces 
+#'  should be considered. Otherwise, only sample-level ones are. 
 #'
 #' @return an object of \code{\link[S4Vectors]{Annotated-class}} that is 
 #' returned by the user provided function with 
@@ -81,8 +83,8 @@
 #' @seealso \url{https://pepkit.github.io/}
 #' @import pepr
 #' @export BiocProject
-BiocProject = function(file, amendments = NULL, autoLoad = TRUE, func = NULL, 
-                       funcArgs = NULL) {
+BiocProject = function(file, amendments = NULL, autoLoad = TRUE, func = NULL,
+                       projectLevel = FALSE, funcArgs = NULL) {
     p = pepr::Project(file=file, amendments = amendments)
     # prevent PEP (Project object) input. This prevents BiocProject object
     # failing when the user provides the Project object
@@ -96,13 +98,15 @@ BiocProject = function(file, amendments = NULL, autoLoad = TRUE, func = NULL,
         }
     }
     args = append(list(p), funcArgs)
-    cfg = pepr::config(p)
+    cfg = .getBiocConfig(p, projectLevel)
+    if(is.null(cfg))
+        cfg = pepr::config(p)
     if(pepr::.checkSection(cfg, c(BIOC_SECTION, FUNCTION_ARGS))){
-        args = .unionList(config(p)[[BIOC_SECTION]][[FUNCTION_ARGS]],args)
+        args = .unionList(config(p)[[BIOC_SECTION]][[FUNCTION_ARGS]], args)
         argsNames = names(args)
         project = args[[.findProjectInList(args)]]
         argsNames = append("",argsNames[-.findProjectInList(args)])
-        args = append(list(p), args[[-.findProjectInList(args)]])
+        args = append(list(p), args[-.findProjectInList(args)])
         names(args) = argsNames
     }
     if (!is.null(func)) {