Initial commit

.github/workflows/CI.yml

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+name: CI
+on:
+  push:
+    branches: [main, master]
+    tags: ["*"]
+  pull_request:
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - "1" # automatically expands to the latest stable 1.x release of Julia
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+          - x86
+        include:
+          # test macOS and Windows with latest Julia only
+          - os: macOS-latest
+            arch: x64
+            version: 1
+          - os: windows-latest
+            arch: x64
+            version: 1
+          - os: windows-latest
+            arch: x86
+            version: 1
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v2
+        with:
+          files: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-docdeploy@latest
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - cron: '00 00 * * *'
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+        run: julia -e 'using CompatHelper; CompatHelper.main(;subdirs=["", "docs"])'

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

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+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+lerna-debug.log*
+node_modules
+dist
+dist-ssr
+*.local
+.vscode/
+!.vscode/extensions.json
+.idea
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
+*.jl.cov
+*.jl.*.cov
+*.jl.mem
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+docs/build/
+docs/site/
+Manifest.toml
+!app/backend/Manifest.toml
+.DS_Store
+out
+build
+draft

CITATION.bib

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+@software{PRISMA.jl,
+  author = {Maples, Ceco Elijah},
+  title  = {PRISMA.jl: Generate checklists and flow diagrams based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)},
+  url    = {https://github.com/cecoeco/PRISMA.jl}
+}

LICENSE.md

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+Copyright 2024 Ceco Elijah Maples
+
+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.

Project.toml

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+name = "PRISMA"
+uuid = "7b67a8d2-c4f5-4933-b91c-0fc427024db5"
+authors = ["Ceco Elijah Maples <mapleselijah9@gmail.com>", "PRISMA.jl Contributors"]
+version = "0.0.6"
+
+[deps]
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
+HTMLTables = "b1afcece-b80e-4563-b90e-36b4cc56d3fa"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+JSONTables = "b9914132-a727-11e9-1322-f18e41205b0b"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Poppler_jll = "9c32591e-4766-534b-9725-b71a8799265b"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+TidierStrings = "248e6834-d0f8-40ef-8fbb-8e711d883e9c"
+Transformers = "21ca0261-441d-5938-ace7-c90938fde4d4"
+XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
+
+[compat]
+CSV = "0.10"
+DataFrames = "1.6"
+DataStructures = "0.18"
+Graphviz_jll = "2.50"
+HTMLTables = "0.4"
+HTTP = "1"
+JSON3 = "1"
+JSONTables = "1"
+LinearAlgebra = "1"
+Poppler_jll = "24.6"
+Statistics = "1"
+TidierStrings = "0.2"
+Transformers = "0.3"
+XLSX = "0.10"
+julia = "1"
+
+[extras]
+HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["HTTP", "Test"]

README.md

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+# PRISMA.jl
+
+<br>
+<div align="center">
+<img src="logo.svg" width="18%">
+</div>
+<br>
+
+Julia package and full-stack [web application](https://prisma-jl.onrender.com) powered by [`Solid.js`](https://www.solidjs.com/) and [`Oxygen.jl`](https://github.com/OxygenFramework/Oxygen.jl) for generating checklists and flow diagrams based on [the 2020 **P**referred **R**eporting **I**tems for **S**ystematic **R**eviews and **M**eta-**A**nalyses (PRISMA) statement (Page et al., 2021).](https://doi.org/10.1186/s13643-021-01626-4)
+
+**Features:**
+
+- natural language processing (NLP) of manuscript PDFs to generate 2020 PRISMA checklists.
+- highly customizable 2020 PRISMA flow diagrams generated from study data.
+- Interactive web app that requires zero programming knowledge.
+
+**Installation:** use this command in the Julia REPL: `using Pkg; Pkg.add("PRISMA")`
+
+**Documentation:** <a href="https://cecoeco.github.io/PRISMA.jl/stable/"><img src="https://img.shields.io/badge/docs-stable-4c9fff.svg" alt="Documentation Stable" /></a> <a href="https://cecoeco.github.io/PRISMA.jl/dev/"><img src="https://img.shields.io/badge/docs-dev-4c9fff.svg" alt="Documentation Dev"></a>
+
+**Citing:** please consider citing PRISMA.jl and giving the GitHub repository a star, if possible.
+
+The citation information may be found in the [`CITATION.bib`](CITATION.bib) file within the repository
+
+**References:**
+
+> Bezanson, J., Edelman, A., Karpinski, S., & Shah, V. B. (2017). Julia: A fresh approach to numerical computing. SIAM Review, 59(1), 65–98. https://doi.org/10.1137/141000671
+
+> Bouchet-Valat, M., & Kamiński, B. (2023). DataFrames.jl: Flexible and Fast Tabular Data in Julia. Journal of Statistical Software, 107(4), 1–32. https://doi.org/10.18637/jss.v107.i04
+
+> Page M J, McKenzie J E, Bossuyt P M, Boutron I, Hoffmann T C, Mulrow C D et al. (2021). The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. Systematic Reviews, 10(1), 89. https://doi.org/10.1186/s13643-021-01626-4

app/backend/Dockerfile

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+FROM julia:1.10
+WORKDIR /backend
+COPY Project.toml Manifest.toml ./
+COPY src src
+RUN julia --project -e "using Pkg; Pkg.instantiate()"
+ENTRYPOINT [ "julia", "--project", "src/app.jl" ]