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https://github.com/aMarcireau/origami

An application to visualize scholar articles as an interactive graph
https://github.com/aMarcireau/origami

doi scholarly-articles science science-research

Last synced: 6 months ago
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An application to visualize scholar articles as an interactive graph

Awesome Lists containing this project

README 

          


    




Origami is an open-source research tool. It automatically scraps Google Scholar pages to retrieve "cited by" papers and presents the results as an interactive graph.



![demo](images/demo.png "A screenshot")



## Download



| [
](https://github.com/aMarcireau/origami/releases/download/v0.11.1/Origami-linux-x64.zip) | [
](https://github.com/aMarcireau/origami/releases/download/v0.11.1/Origami-darwin-x64.zip) | [
](https://github.com/aMarcireau/origami/releases/download/v0.11.1/Origami-win32-x64.zip) |

| ------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------- |

| [Download for Linux](https://github.com/aMarcireau/origami/releases/download/v0.11.1/Origami-linux-x64.zip)                                                   | [Download for macOS](https://github.com/aMarcireau/origami/releases/download/v0.11.1/Origami-darwin-x64.zip)                                                   | [Download for Windows](https://github.com/aMarcireau/origami/releases/download/v0.11.1/Origami-win32-x64.zip)                                                   |



Visit the [Releases](https://github.com/aMarcireau/origami/releases) page to download Origami for other platforms.



## Color theme



To change the color theme, edit `colors.json`. You can find it at:



-   `Origami/resources/app/colors.json` on Linux

-   `Origami.app/Contents/Resources/app/colors.json` on macOS (right-click on the app and choose _Show Package Contents_)

-   `Origami\resources\app\colors.json` on Windows



The `themes` directory of this repository contains several themes suggestions.



## Formats



### Multiple DOIs import



Origami can load several DOIs at once from a [JSON](https://www.json.org) formated file with the following structure:



```yaml

[

    "10.1109/biorob.2016.7523449",

    "10.3389/fnins.2017.00350",

    "10.3389/fnins.2017.00535",

    "10.1109/tbcas.2017.2759700",

    "10.3389/fnins.2016.00594",

    "10.1007/s11263-017-1050-6"

]

```



### Saves



Origami saves and loads collections in [JSON](https://www.json.org) format. The generated files have the following structure:



```yaml

{

  "appVersion": "0.11.1", # the version of the app used to generate this save

  "display": 0, # the current display's index (0 for graph, 1 for list)

  "knownDois": ["10.1109/tpami.2016.2574707"], # list of DOIs clicked at least once (used to highlight new publications)

  "crossref": # pending requests to crossref.org

    [

      {

        "type": "CROSSREF_REQUEST_TYPE_VALIDATION",

        "doi": "10.1038/nature06293"

      },

      {

        "type": "CROSSREF_REQUEST_TYPE_CITER_METADATA",

        "parentDoi": "10.1109/tpami.2016.2574707",

        "title": "A Motion-Based Feature for Event-Based Pattern Recognition",

        "authors": ["X Clady", "JM Maro", "S Barré", "RB Benosman"],

        "dateAsString": "2017"

      },

      {

        "type": "CROSSREF_REQUEST_TYPE_IMPORTED_METADATA",

        "title": "EMVS: Event-Based Multi-View Stereo—3D Reconstruction with an Event Camera in Real-Time",

        "authors":

          [

            "Henri Rebecq",

            "Guillermo Gallego",

            "Elias Mueggler",

            "Davide Scaramuzza"

          ],

        "dateAsString": "2017"

      }

    ],

  "doi": [{ "doi": "10.1038/nature06293" }], # pending requests to doi.org

  "scholar": [ # pending requests to scholar.google.com

      "requests":

        [

          {

            "type": "SCHOLAR_REQUEST_TYPE_INITIALIZE",

            "doi": "10.3389/fnins.2016.00594",

            "url": "https://scholar.google.com/scholar?hl=en&q=10.3389%2Ffnins.2016.00594"

          },

          {

            "type": "SCHOLAR_REQUEST_TYPE_CITERS",

            "doi": "10.1109/biorob.2016.7523449",

            "url": "https://scholar.google.com/scholar?cites=3831926773876645447&start=0&hl=en",

            "number": 1,

            "total": 1

          }

        ],

      "minimumRefractoryPeriod": 2000, # minimum waiting time between scholar requests, in milliseconds

      "maximumRefractoryPeriod": 8000 # maximum waiting time between scholar requests, in milliseconds

    ],

  "graph": {

      "threshold": 1, # the current threshold used to filter suggestions, non-zero integer

      "zoom": 0, # the current zoom level, integer in the range [-50, 50]

      "xOffset": 0, # the current graph positions' x coordinate, float

      "yOffset": 0, # the current graph positions' y coordinate, float

      "sticky": false # false means that the 'sticky' box is unchecked

    },

  "publications": [ # list of known publications

      [

        # each publication is a two-elements list containg a string and an object

        "10.1109/tpami.2016.2574707", # the publication's DOI

        {

          # object containing the publication's data

          "status":

            "PUBLICATION_STATUS_IN_COLLECTION" # the publication's status in Origami, which can be:

            #     "PUBLICATION_STATUS_UNVALIDATED": the DOI was added, but not validated

            #     "PUBLICATION_STATUS_DEFAULT": suggested publication

            #     "PUBLICATION_STATUS_IN_COLLECTION": in-collection publication,

          "title": "HOTS: A Hierarchy of Event-Based Time-Surfaces for Pattern Recognition",

          "authors":

            [

              "Xavier Lagorce",

              "Garrick Orchard",

              "Francesco Galluppi",

              "Bertram E. Shi",

              "Ryad B. Benosman"

            ],

          "journal": "Institute of Electrical and Electronics Engineers (IEEE)",

          "date": [2016, 7, 14], # the publication's release date, list of one to three integer values (optional month and day)

          "citers":

            [

              "10.1109/biorob.2016.7523449",

              "10.3389/fnins.2017.00350",

              "10.3389/fnins.2017.00535",

              "10.1109/tbcas.2017.2759700",

              "10.3389/fnins.2016.00594",

              "10.1007/s11263-017-1050-6"

            ],

          "updated": 1513430331442, # last metadata update, in milliseconds since 1970-01-01

          "selected":

            false # false means that the publication is not selected

                  # only one publication can be selected

          "bibtex": "@article{...}", # the article's BibTeX as a string

          "x": 1.0813568646326681, # the publication's node position's x coordinate in the graph, float

          "y": -1.563450690825733, # the publication's node position's y coordinate in the graph, float

          "locked": false, # false means that the publication's node's position is not stuck

        }

      ]

    ],

  "search": "", # the current regular expression in the search input

  "tabs": 0, # the active tab (0 for information, 1 for search, 2 for warnings)

  "warnings": # list of warnings

    [

      {

        "title": "The Crossref request for 'Poker-DVS and MNIST-DVS. Their history, how they were made, and other details' failed",

        "subtitle": "The returned article was older than the cited one (10.1109/tpami.2016.2574707)",

        "level": "warning"

      }

    ]

}

```



## Contribute



### Install



Origami is build with [Electron](https://electronjs.org), [React](https://reactjs.org) and [Redux](https://redux.js.org).



Follow these steps to download the source code, edit and build Origami:



1. install [Node.js](https://nodejs.org)

2. clone the repository by running from a terminal `git clone https://github.com/aMarcireau/origami.git`

3. go to the created _origami_ folder and run `npm install`



For development, run the command `npm run-script watch` from the _origami_ folder. A development build is triggered every time a file in the _souce_ directory is modified.



To create a new release:



1. create a personal access token (see https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)

2. create a file auth.json in the _origami_ directory with the following structure:



```json

{

    "username": "Github username",

    "token": "personal access token"

}

```



3. generate a production build for each supported platform with `npm run-script build`

4. create a new Github release (requires administration rights on this repository) with `npm run-script release`



To build Windows apps with macOS Catalina, one must patch Wine (see https://github.com/electron/node-rcedit/issues/51#issuecomment-546234084).



Code documentation: [Wiki](https://github.com/aMarcireau/origami/wiki).



## License



See the [LICENSE](LICENSE.txt) file for license rights and limitations (MIT).