putting frontend and backend on same domain

.gitignore

@@ -28,7 +28,8 @@ deps/src/
 docs/build/
 docs/site/
 Manifest.toml
-*.DS_Store
+!app/Manifest.toml
+.DS_Store
 out
 build
 draft

Project.toml

@@ -14,24 +14,12 @@ TidierStrings = "248e6834-d0f8-40ef-8fbb-8e711d883e9c"
 Transformers = "21ca0261-441d-5938-ace7-c90938fde4d4"
 
 [compat]
-CSV = "0.10"
 DataFrames = "1.6"
 DataStructures = "0.18"
-HTMLTables = "0.4"
 Graphviz_jll = "2.50"
 LinearAlgebra = "1"
 Poppler_jll = "24.6"
 Statistics = "1"
 TidierStrings = "0.2"
 Transformers = "0.3"
-XLSX = "0.10"
 julia = "1"
-
-[extras]
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-HTMLTables = "b1afcece-b80e-4563-b90e-36b4cc56d3fa"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
-
-[targets]
-test = ["Test", "CSV", "HTMLTables", "XLSX"]

README.md

@@ -2,17 +2,27 @@
 
 <br>
 <div align="center">
-<img src="docs/src/assets/logo.svg" width="17%">
+<img src="logo.svg" width="17%">
 </div>
 <br>
 
-Julia package and [web application](https://prisma-jl.onrender.com) built with [`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)
+Julia package and [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)
 
-:arrow_down: **Installation:** use this command in the Julia REPL: `using Pkg; Pkg.add("PRISMA")`
+**Features:**
 
-:book: **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>
+- natural language processing (NLP) of manuscript PDFs to generate completed 2020 PRISMA checklists.
+- highly customizable 2020 PRISMA flow diagrams generated from study data.
+- Interactive web app that requires zero programming knowledge.
 
-:books: **References:**
+**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
 

app/Dockerfile

@@ -0,0 +1,5 @@
+FROM julia:1.10
+WORKDIR /app
+COPY . .
+RUN julia --project -e "using Pkg; Pkg.instantiate()"
+ENTRYPOINT [ "julia", "--project", "src/app.jl" ]

app/backend/Project.toml → app/Project.toml

@@ -4,6 +4,8 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 HTMLTables = "b1afcece-b80e-4563-b90e-36b4cc56d3fa"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSONTables = "b9914132-a727-11e9-1322-f18e41205b0b"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+NodeJS = "47edcb42-4c32-5a88-959f-defineb9c2f8b290"
 Oxygen = "df9a0d86-3283-4920-82dc-4555fc0d1d8b"
 PRISMA = "7b67a8d2-c4f5-4933-b91c-0fc427024db5"
 
@@ -13,6 +15,8 @@ DataFrames = "1"
 HTMLTables = "0.4"
 HTTP = "1"
 JSONTables = "1"
+JSON3 = "1"
+NodeJS = "2"
 Oxygen = "1"
 PRISMA = "0.0.5"
 julia = "1"

app/frontend/src/pages/checklist.tsx → app/frontend/pages/checklist.tsx

@@ -76,7 +76,7 @@ export default function Checklist() {
     formData.append("file", file());
     try {
       const response = await fetch(
-        "https://prisma-jl-api.onrender.com/checklist/generate",
+        "https://prisma-jl.onrender.com/api/checklist/generate",
         {
           method: "POST",
           body: formData,
@@ -249,7 +249,7 @@ export default function Checklist() {
     }));
     try {
       const response = await fetch(
-        "https://prisma-jl-api.onrender.com/checklist/export",
+        "https://prisma-jl.onrender.com/api/checklist/export",
         {
           method: "POST",
           headers: { "Content-Type": "application/json" },

app/frontend/src/pages/flow_diagram.tsx → app/frontend/pages/flow_diagram.tsx

@@ -371,7 +371,7 @@ export default function FlowDiagram() {
   async function getFlowDiagram() {
     try {
       const response = await fetch(
-        "https://prisma-jl-api.onrender.com/flow_diagram/generate",
+        "https://prisma-jl.onrender.com/api/flow_diagram/generate",
         {
           method: "POST",
           headers: { "Content-Type": "application/json" },
@@ -414,7 +414,7 @@ export default function FlowDiagram() {
   async function downloadFlowDiagram() {
     try {
       const response = await fetch(
-        "https://prisma-jl-api.onrender.com/flow_diagram/export",
+        "https://prisma-jl.onrender.com/api/flow_diagram/export",
         {
           method: "POST",
           headers: { "Content-Type": "application/json" },

app/frontend/index.html → app/index.html

@@ -4,7 +4,7 @@
 <head>
 	<meta charset="utf-8" />
 	<meta name="viewport" content="width=device-width, initial-scale=1" />
-	<link rel="icon" type="image/x-icon" href="favicon.ico" />
+	<link rel="icon" type="image/x-icon" href="frontend/assets/favicon.ico" />
 	<title>PRISMA.jl</title>
 	<meta name="description" content="PRISMA.jl: generate checklists and flow diagrams based on the PRISMA statement" />
 	<meta name="theme-color" media="(prefers-color-scheme: light)" content="hsl(210, 100%, 98%)" />
@@ -14,7 +14,7 @@
 <body>
 	<noscript>You need to enable JavaScript to run this app.</noscript>
 	<div id="root"></div>
-	<script src="src/index.tsx" type="module"></script>
+	<script src="frontend/index.tsx" type="module"></script>
 </body>
 
 </html>