re

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+LICENSE.md

.github/.gitignore

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+*.html

.github/workflows/check-standard.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - 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@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+README.Rmd

DESCRIPTION

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+Package: puremoe
+Type: Package
+Title: Pubmed Unified REtrieval for Multi-Output Exploration
+Version: 1.0.0
+Author: Jason Timm [aut, cre]
+Maintainer: Jason Timm <JaTimm@salud.unm.edu>
+Description: An R package for accessing a variety of PubMed data, including abstracts, bibliometrics, pubtations, and full-text records, through a single, user-friendly interface.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: false
+Depends: 
+    R (>= 3.5)
+Imports: 
+    rentrez,
+    textshape,
+    xml2,
+    data.table,
+    httr,
+    pbapply,
+    jsonlite,
+    rappdirs
+Suggests: 
+    knitr,
+    rmarkdown
+RoxygenNote: 7.3.1

LICENSE

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+YEAR: 2022
+COPYRIGHT HOLDER: Jason Timm

LICENSE.md

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+# MIT License
+
+Copyright (c) 2022 Jason Timm
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(data_mesh_embeddings)
+export(data_mesh_thesuarus)
+export(data_mesh_trees)
+export(data_pharm_action)
+export(data_pmc_list)
+export(get_records)
+export(search_pubmed)
+import(data.table)
+importFrom(data.table,fread)
+importFrom(data.table,rbindlist)
+importFrom(data.table,setDT)
+importFrom(httr,GET)
+importFrom(httr,content)
+importFrom(jsonlite,stream_in)
+importFrom(parallel,clusterExport)
+importFrom(parallel,detectCores)
+importFrom(parallel,makeCluster)
+importFrom(parallel,stopCluster)
+importFrom(pbapply,pblapply)
+importFrom(rappdirs,user_data_dir)
+importFrom(rentrez,entrez_fetch)
+importFrom(rentrez,entrez_search)
+importFrom(utils,download.file)
+importFrom(utils,read.csv)
+importFrom(utils,untar)
+importFrom(xml2,read_xml)
+importFrom(xml2,xml_children)
+importFrom(xml2,xml_find_all)
+importFrom(xml2,xml_find_first)
+importFrom(xml2,xml_text)

R/data_mesh_embeddings.R

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+#' Download and Process Mesh and SCR Embeddings
+#'
+#' This function downloads Mesh and SCR embeddings data from the specified URLs and processes it for use.
+#' The data is saved locally in RDS format. If the files do not exist, they will be downloaded and processed.
+#'
+#' @return A data frame containing the processed Mesh and SCR embeddings data.
+#'
+#' @importFrom rappdirs user_data_dir
+#' @importFrom utils download.file
+#' @export
+#' @examples
+#' \donttest{
+#' if (interactive()) {
+#'   # Code that downloads data or performs other interactive-only operations
+#'   data <- data_mesh_embeddings()
+#' }
+#' }
+
+#' 
+data_mesh_embeddings <- function() {
+
+  # Define the URLs for Mesh and SCR embeddings data
+  sf <- 'https://github.com/jaytimm/mesh-builds/blob/main/data/data_mesh_embeddings.rds?raw=true'
+  sf2 <- 'https://github.com/jaytimm/mesh-builds/blob/main/data/data_scr_embeddings.rds?raw=true'
+
+  # Define local file paths for storing the processed data
+  df <- file.path(rappdirs::user_data_dir('puremoe'), 'data_mesh_embeddings.rds')
+  df2 <- file.path(rappdirs::user_data_dir('puremoe'), 'data_scr_embeddings.rds')
+
+  # Check if the directory for data storage exists, and create it if not
+  if (!dir.exists(rappdirs::user_data_dir('puremoe'))) {
+    dir.create(rappdirs::user_data_dir('puremoe'), recursive = TRUE)
+  }
+
+  # Download and process Mesh embeddings data if it doesn't exist
+  if (!file.exists(df)) {
+    message('Downloading the Mesh embeddings ...')
+    out <- tryCatch({
+      utils::download.file(sf, df)
+    }, error = function(e) paste("Error"))
+
+    if (out == 'Error') {
+      message('Download not completed ... Try options(timeout = 600)')
+      file.remove(df)
+    }
+  }
+
+  # Download and process SCR embeddings data if it doesn't exist
+  if (!file.exists(df2)) {
+    message('Downloading the SCR embeddings ...')
+    out <- tryCatch({
+      utils::download.file(sf2, df2)
+    }, error = function(e) paste("Error"))
+
+    if (out == 'Error') {
+      message('Download not completed ... Try options(timeout = 600)')
+      file.remove(df2)
+    }
+  }
+
+  # If both files exist, read and combine them
+  if (all(file.exists(df), file.exists(df2))) {
+    a1 <- readRDS(df)
+    a2 <- readRDS(df2)
+
+    result <- rbind(a1, a2)
+    return(result)
+  }
+
+  return(NULL)
+}

R/data_mesh_thesaurus.R

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+#' Download and Combine MeSH and Supplemental Thesauruses
+#'
+#' This function downloads and combines the MeSH (Medical Subject Headings) Thesaurus 
+#' and a supplemental concept thesaurus for use in biomedical research and analysis.
+#' The data is sourced from specified URLs and stored locally for subsequent use.
+#' @param force_download A logical value indicating whether to force re-downloading 
+#' of the data even if it already exists locally.
+#' @return A data.table containing the combined MeSH and supplemental thesaurus data.
+#' @importFrom rappdirs user_data_dir
+#' @importFrom utils download.file
+#' @importFrom data.table rbindlist
+#' @export
+#' @examples
+#' \donttest{
+#' if (interactive()) {
+#'   # Code that downloads data or performs other interactive-only operations
+#'   data <- data_mesh_thesaurus()
+#' }
+#' }
+
+
+data_mesh_thesuarus <- function(force_download = FALSE) {
+
+  # URLs for the MeSH thesaurus and supplemental thesaurus data
+  sf <- 'https://github.com/jaytimm/mesh-builds/blob/main/data/data_mesh_thesaurus.rds?raw=true'
+  sf2 <- 'https://github.com/jaytimm/mesh-builds/blob/main/data/data_scr_thesaurus.rds?raw=true'
+
+  # Local file paths for storing the downloaded data
+  df <- file.path(rappdirs::user_data_dir('puremoe'), 'data_mesh_thesuarus.rds')
+  df2 <- file.path(rappdirs::user_data_dir('puremoe'), 'data_scr_thesuarus.rds')
+
+  # Check for the existence of the files or force download
+  if (!file.exists(df) | force_download) {
+    # Create the directory if it doesn't exist
+    if (!dir.exists(rappdirs::user_data_dir('puremoe'))) {
+      dir.create(rappdirs::user_data_dir('puremoe'), recursive = TRUE)
+    }
+
+    # Download the MeSH thesaurus data
+    message('Downloading the mesh thesaurus ...')
+    utils::download.file(sf, df, mode = "wb")
+  }
+
+  # Repeat the process for the supplemental concept thesaurus
+  if (!file.exists(df2) | force_download) {
+    message('Downloading the supplemental concept thesaurus ...')
+    utils::download.file(sf2, df2, mode = "wb")
+  }
+
+  # Read the downloaded RDS files
+  a1 <- readRDS(df)
+  a2 <- readRDS(df2)
+
+  # Ensure the column names are consistent between the two data sets
+  colnames(a2) <- colnames(a1)
+
+  # Combine the data using data.table's rbindlist
+  data.table::rbindlist(list(a1, a2))
+}