update readme and app frontend styles

README.md

@@ -1,55 +1,90 @@
-# PRISMA.jl
+## PRISMA.jl
+
+<div align="center"><img src="docs/src/assets/logo.svg" width="130">
+</div>
+
+PRISMA.jl is a Julia package and [web application]() for generating checklists and flow diagrams based on the [the **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)
+
+### :book: Documentation
 
 <div>
-  </br>
-  <p align="center"><img src="docs/src/assets/logo.svg" width="130"></p>
-  <p align="center"><strong><i>checklists and flow diagrams for evidence syntheses</i></strong></p>
-  <div align="center">
-  <a href="https://github.com/cecoeco/PRISMA.jl/blob/main/LICENSE.md"><img alt="License: MIT" src="https://img.shields.io/badge/License-MIT-yellow.svg"></a>
-  <a href="https://github.com/JuliaDiff/BlueStyle"><img alt="Style: Blue" src="https://img.shields.io/badge/code%20style-blue-4495d1.svg"></a>
-  <a href="https://github.com/cecoeco/PRISMA.jl/actions/workflows/CI.yml"><img src="https://github.com/cecoeco/PRISMA.jl/actions/workflows/CI.yml/badge.svg" alt="CI" /></a>
-  <a href="https://cecoeco.github.io/PRISMA.jl/dev/"><img src="https://img.shields.io/badge/docs-dev-royalblue.svg" alt="Documentation Development" /></a>
-  <a href="https://juliapkgstats.com/pkg/PRISMA"><img src="https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Fmonthly_downloads%2FPRISMA&query=total_requests&suffix=%2Fmonth&label=Downloads" alt="Package Statistics"></a>
-  <a href="https://www.contributor-covenant.org"><img src="https://img.shields.io/badge/Contributor%20Covenant-v2.1%20adopted-ff69b4.svg" alt="Contributor Covenant"></a>
-  </div>
+<a href="https://cecoeco.github.io/PRISMA.jl/stable/"><img src="https://img.shields.io/badge/docs-stable-royalblue.svg" alt="Documentation Stable" /></a>
+<a href="https://cecoeco.github.io/PRISMA.jl/dev/"><img src="https://img.shields.io/badge/docs-dev-royalblue.svg" alt="Documentation Dev"></a>
 </div>
 
-## About
+### :arrow_down: Installation
+
+```julia
+using Pkg; Pkg.add("PRISMA")
+```
 
-PRISMA.jl is a Julia-based software package that generates checklists and flow diagrams for systematic reviews and meta-analyses based on [the <b>P</b>referred <b>R</b>eporting <b>I</b>tems for <b>S</b>ystematic <b>R</b>eviews and <b>M</b>eta-<b>A</b>nalyses (PRISMA) statement (Page et al., 2021).](https://doi.org/10.1186/s13643-021-01626-4) Its companion web application can also be used by researchers with little to no programming experience looking to report the results from their systematic reviews and meta-analyses with efficiency and transparency: [Link coming soon.]()
+### Examples
 
-## Installation
+creating a completed checklist from a paper and
+saving the results to a spreadsheet:
 
 ```julia
-import Pkg; Pkg.add("PRISMA")
+using PRISMA: Checklist, checklist
+using DataStructures: LittleDict
+using XLSX: writetable
+
+clist::Checklist = checklist("manuscript.pdf")
+
+println(clist)
+
+clist_metadata::LittleDict = clist.metadata
+
+println(clist_metadata)
+
+title::String = clist_metadata["title"]
+
+println(title)
+
+writetable("$title.xlsx", title => clist.df)
 ```
 
-If you do not have Julia or a text-editor that supports Julia installed, then you might find this [link](https://julialang.org/learning/) helpful before getting started.
+the `checklist_df` function can be used to create spreadsheet files that can be edited outside Julia programs:
+
+```julia
+using PRISMA: checklist_df
+using DataFrames: DataFrame
+using XLSX: writetable
 
-## Example
+clist_template::DataFrame = checklist_df()
 
-This simple example shows how a few functions in this package can be used together to create a flow diagram:
+println(clist_template)
 
-```Julia
-using PRISMA
+writetable("PRISMA_checklist.csv", "sheet_1" => clist_template)
+```
+
+the `DataFrame` that is created from the `checklist_df` function can also be edited within a Julia program using functions from the `DataFrames` package:
+
+```julia
+using PRISMA: checklist_df
+using DataFrames: DataFrame
 
-# The flow_diagram_csv() function generates a csv template.
-# The path of the template is assigned to the "data" variable,
-# but in most scenarios the template is edited before it is assigned and read.
-data = PRISMA.flow_diagram_csv()
+clist_template::DataFrame = checklist_df()
 
-# The flow_diagram_read() function reads the csv saved as "data"
-# and turns it into a dataframe and assigns it to "df".
-df = PRISMA.flow_diagram_read(file=data)
+println(clist_template)
 
-# The flow_diagram() function turns data frames into
-# flow diagrams that show the results of a meta-analysis or systematic review.
-figure = PRISMA.flow_diagram(data=df)
+clist_template[3, "Location where item is reported"] = "Sysemtatic review is in the title."
+clist_template[5, "Location where item is reported"] = "The completed abastract is located on page one."
 
-# The flow_diagram_save() function saves the figure and saves
-# it in formats supported by Makie.jl, png is the default.
-PRISMA.flow_diagram_save(figure=figure)
+println(clist_template)
 ```
 
-Result:
-![flow diagram](docs/src/assets/figure.svg)
+The `DataFrame` from a `Checklist` can still be edited after the paper is read by access the `df` field from the `Checklist` type:
+
+```julia
+using PRISMA: Checklist, checklist
+using DataFrames: DataFrame
+
+clist::Checklist = checklist("manuscript.pdf")
+
+clist_df::DataFrame = clist.df
+
+clist_df[3, "Location where item is reported"] = "Sysemtatic review is in the title."
+clist_df[5, "Location where item is reported"] = "The completed abastract is located on page one."
+
+println(clist_df)
+```

app/backend/Project.toml

@@ -8,6 +8,7 @@ HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 JSONTables = "b9914132-a727-11e9-1322-f18e41205b0b"
 Oxygen = "df9a0d86-3283-4920-82dc-4555fc0d1d8b"
+PRISMA = "7b67a8d2-c4f5-4933-b91c-0fc427024db5"
 
 [compat]
 julia = "1.10"

app/backend/app.jl

@@ -51,8 +51,8 @@ end
 Oxygen.post("/flow_diagram") do req::HTTP.Request
     flow_diagram_options::JSON3.Object = JSON3.read(String(req.body))
 
-    flow_diagram_dot::PRISMA.FlowDiagram = PRISMA.flow_diagram(
-        DataFrame(JSONTables.jsontable(flow_diagram_options["json"])),
+    flow_diagram_gv::PRISMA.FlowDiagram = PRISMA.flow_diagram(
+        DataFrame(JSONTables.jsontable(flow_diagram_options["data"])),
 
         background_color =   flow_diagram_options["background_color"],
         grayboxes =          flow_diagram_options["grayboxes"],
@@ -78,7 +78,12 @@ Oxygen.post("/flow_diagram") do req::HTTP.Request
         arrow_width =        flow_diagram_options["arrow_width"]
     )
 
-    return Oxygen.json(Dict{String,String}("dot" => flow_diagram_dot.dot))
+    tempname_svg::String = tempname() * ".svg"
+    PRISMA.flow_diagram_save(tempname_svg, flow_diagram_gv)
+    svg::String = read(tempname_svg, String)
+    rm(tempname_svg)
+
+    return Oxygen.json(Dict{String,String}("svg" => svg))
 end
 
 Oxygen.serve(host="0.0.0.0", port=5050, docs=false, middleware=[corshandler])