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aMarcireau / origami

An application to visualize scholar articles as an interactive graph
MIT License
19 stars 1 forks source link
doi scholarly-articles science science-research

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

Download
Download for Linux Download for macOS Download for Windows

Visit the Releases page to download Origami for other platforms.

Color theme

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

The themes directory of this repository contains several themes suggestions.

Formats

Multiple DOIs import

Origami can load several DOIs at once from a JSON formated file with the following structure:

[
    "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 format. The generated files have the following structure:

{
  "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, React and Redux.

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

  1. install Node.js
  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:
{
    "username": "Github username",
    "token": "personal access token"
}
  1. generate a production build for each supported platform with npm run-script build
  2. 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.

License

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