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    ro-crate-excel

    1.0.10 • Public • Published

    ro-crate-excel

    Node library with utilities for converting RO-Crates to Spreadsheet format for data entry and vice versa

    THis replaces the Calcyte tool, both the javascript and previous Python versions.

    What is this?

    This is a library for building tools to assist in JSON-lD data entry, it has been built for RO-Crate but could be used for more general purpose JSON-LD <-> Spreadsheet conversion.

    Installation

    To use the script

    npm install rocxl --global

    For development

    Get this repository (assuming you are working in ~/working):

    git clone https://github.com/UTS-eResearch/ro-crate-excel.git ~/working/ro-crate-excel

    Change into the directory: cd ~/working/ro-crate-excel

    Install the app:

    npm install . npm link # to install the rocxl script

    Run the tests:

    mocha

    Usage

    To run this code use the rocxl (Excel <-> Research Object) script.

    rocxl creates RO-Crates with an HTML entry-point in ro-crate-preview.html file.

    Usage:

    ./rocxl 
    Usage: rocxl [options] <directories...>
    

    Generates an an excel spreadsheet and RO-Crate metadata from a set of files and updates the RO-Crate with data filled in the spreadsheet.

    To generate an excel spreadsheet from an ro-crate-metadata.json file instead, use the --JSON option.

    The file system is ALWAYS traversed and file information merged into existing metadata.

    
    Options:
      -V, --version                    output the version number
      -b,  --bag [bag-dir]             Create Bagit Bag(s) under [bag-dir])
      -z   --zip                       Zip the bagged ro-crate (only works with --bag
      -j   --JSON                      Use the ro-crate-metafata.json file rather than ro-crate-metadata.xslx
      -p   --partOf [partOf]           This is part of another RO-Crate, supply the ro-crate-metadata.json path.
      -d,  --depth [depth]             Maximum depth to recurse into directories looking for files
      -r,  --recurse                   Recurse into directories looking for files
      -c,  --cratescript [cratesript]  URL of Crate-script directory
      -m,  --maxfiles [maxfiles]       Maximum number of files to itemise per directory (default is undefined)
      -u, --url [distro]               Distribution URL
      -h, --help                       output usage information
    

    To run rocxl on a group of directories pass it a list of directories

    One directory:

    
    rocxl test_data/Glop_Pot -r
    

    This will:

    • Traverse the entire Glop_Pot directory, and generate or update the ro-crate-metadata.xlsx files.
    • Create or update the test_data/Glop_Pot/ro-crate-metadata.json`` file
    • Create a [RO-Crate] Website with entry-point test_data/Glop_Pot/ro-crate-metadata.html

    All the sample directories:

    rocxl -r test_data/* -c https://data.research.uts.edu.au/examples/ro-crate/examples/src/crate.js
    

    rocxl will generate:

    • a ro-crate-metadata.xlsx file in each root directory (this is for humans to fill in with metadata about the data)

    • An ro-crate-metadata.json file containing JSON-LD metadata derived from the spreadsbeet some basic file-format information.

    • An ro-crate-preview.html file generated from ro-crate-metadata.json

    See the examples in test_data.

    About the spreadsheet format

    This library allows transformation between RO-Crate and Excel spreadsheets using multiple worksheets in a workbook which is named 'ro-crate-metadata.xslx' and appears alongside the ro-crate-metadata.json file in the root of the dataset.

    The Root Dataset Worksheet

    The root dataset item is represented by a worksheet named "RootDataset" referred to as the Root Dataset Worksheet; this worksheet has two columns, Name and Value. Each value of a property is represented as a row in the spreadsheet.

    For example - the worksheet for this Dataset:

    {
        "@id": "./",
       "@type": "Dataset",
        "datePublished": "2017",
        "name": "Example Dataset",
        "identifier": "https://doi.org/10.4225/59/59672c09f4a4b", 
        "description": "Do try to put more info in here than the title. Please.",
        "author": [{"@id": "https://orcid.org/0000-0002-3545-944X"}, {"@id": "https://orcid.org/0000-0001-5152-5307"}],
        "license": {"@id": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/"}
     }
    

    Is structured as per this table

    Name Value
    @id ./
    @type Dataset
    name Example Dataset
    description Do try to put more info in here than the title. Please.
    author "Peter Sefton"
    author "Michael Lynch"
    license "https://creativecommons.org/licenses/by-nc-sa/3.0/au/"

    Multiple values use multiple lines

    The multi-valued author property is represented as two rows as this is convenient to do in this vertically aligned Name/Value format.

    References

    The quotes around the Values for license and author indicate that the value is a reference to another item - these references can be to the name or @id property of the item. If the license and person items are JSON-LD items like these:

    {
      "@id": "https://creativecommons.org/licenses/by/4.0/",
      "@type": "CreativeWork",
      "name": "CC BY 4.0",
      "description": "Creative Commons Attribution 4.0 International License"
    },
    {
          "@id": "http://orcid.org/0000-0002-3545-944X",
          "@type": "Person",
          "name": "Peter Sefton",
          "familyName": "Sefton",
          "givenName": "Peter",
          "affiliation": {
            "@id": "https://ror.org/0384j8v12"
          }
        }
    
        {
          "@id": "https://orcid.org/0000-0001-5152-5307",
          "@type": "Person",
          "name": "Michael Lynch",
          "familyName": "Lynch",
          "givenName": "Michael",
          "affiliation": {
            "@id": "https://ror.org/0384j8v12"
          }
              }
    
    

    Then the Person and the CreativeWork will be described in two additional worksheets named @type=Person and @type=CreativeWork, these Type Worksheets use a different format to represent one item per line.

    The @type=Person worksheet is as follows:

    @id @type name FamilyName givenName affiliation
    http://orcid.org/0000-0002-3545-944X Person Peter Sefton Sefton Peter "https://ror.org/0384j8v12"
    https://orcid.org/0000-0001-5152-5307 Person Michael Lynch Lynch Michael "https://ror.org/0384j8v12"

    And the @type=CreativeWork worksheet:

    @id @type name description
    https://creativecommons.org/licenses/by/4.0/ CreativeWork CC BY 4.0 Creative Commons Attribution 4.0 International License

    Representing multiple values

    To represent multiple values - for example if there are multiple affiliations for a person then a comma separated list enclosed in square brackets.

    @id @type name FamilyName givenName affiliation
    http://orcid.org/0000-0002-3545-944X Person Peter Sefton Sefton Peter ["https://ror.org/0384j8v12", http://ptsefton.com]

    This approach can also be used in the Root Dataset Worksheet. The URL is treated as a string value as it is not enclosed in double quotes.

    Name Value
    author ["Peter Sefton", http://ptsefton.com]

    These values will be interpreted as references, omitting the quotes will cause a value to be interpreted as a string.

    Embedding JSON

    To avoid having to create @type Worksheets for things such as GeoCoordinates or PropertyVale items, items, or arrays of items may be embedded in a cell using standard JSON-LD.

    For example, this Place item:

    {
          "@id": "http://www.geonames.org/8152662/catalina-park.html",
          "@type": "Place",
          "address": "Katoomba, NSW",
          "description": "Catalina Park is a disused motor racing venue, located at Katoomba, in the Blue Mountains, New South Wales, Australia, and is recognised as an Aboriginal Place due to the long association of the local Gundungarra and Darug clans to the area.",
          "geo": {
            "@id": "#d2c5b5e0-a720-4b21-ad3a-f44ad89488e7"
          },
          "name": "Catalina Park"
        }
    

    Can be represented in the @type=Place worksheet:

    @id @type address description geo name
    http://www.geonames.org/8152662/catalina-park.html Place Katoomba, NSW Catalina Park is a disused motor racing venue, located at Katoomba, in the Blue Mountains, New South Wales, Australia, and is recognised as an Aboriginal Place due to the long association of the local Gundungarra and Darug clans to the area. {"@id":"#d2c5b5e0-a720-4b21-ad3a-f44ad89488e7","@type":"GeoCoordinates","latitude":"-33.7152","longitude":"150.30119","name":"Latitude: -33.7152, Longitude: 150.30119"} Catalina Park

    NOTE: Any cell that contains at least one { and one } will be parsed as JSON - if that fails it will be included as an escaped string.

    Adding additional properties to the @context

    There are reasons to add additional properties.

    If the URL for a property does not resolve to a useful URL.

    In this case define an item of @type Property in the @type=Property worksheet (or if you're starting with a crate, add an item of @type Property to the graph.) The @id should be the URL of the fully resolved property - to use the example from the spec

    @id @type name description sameAs
    http://purl.org/ontology/bibo/interviewee Property http://neologism.ecs.soton.ac.uk/bibo.html#interviewee

    { "@context": [ "https://w3id.org/ro/crate/1.0/context", {"interviewee": "http://purl.org/ontology/bibo/interviewee"}, ], "@graph": [ { "@id": "http://purl.org/ontology/bibo/interviewee", "sameAs": "http://neologism.ecs.soton.ac.uk/bibo.html#interviewee", "@type": "Property" } ] }

    If the property is locally defined

    To define a local property which is specific to a dataset or because there is no available public ontology that has one - define it in the graph as an item of @type rdf:Property, as per the RO-Crate Spec advice on ad hoc terms.

    { "@context": [ "https://w3id.org/ro/crate/1.0/context", {"myProp": "https://w3id.org/ro/terms/myNameSpace/#myProp"}, ], "@graph": [ { "@id": "https://w3id.org/ro/terms/myNameSpace/#myProp", "@type": "rdf:Property", "rdfs:label": "myProp", "rdfs:comment": "This is my custom property I want to use in describing things" } ] }

    Which on conversion to Excel would look like:

    @id @type rdfs:label rdfs:comment sameAs
    _:myProp myProp This is my custom property I want to use in describing things

    TODO: Make @context entries for additional Property items automatically show up in the @context if not already defined - and force appropriate IDs (they must be either full http(s) URIs or blank node @ids and start with a lowercase letter).

    Implementing Workbook to RO-Crate

    When converting from a worksheet to a JSON-LD item the process is to:

    • Convert the Root DataSet Workseet to an RO Crate Root Dataset - with the necessary @id and other

    • Convert each @type sheet to an item by mapping column names to properties; each row becomes an item in the RO-Crate graph.

    • Index the crate by @id and by name

    • For every item in the @graph array:

    • Normalise the item's @id: - If the @id is a URL, or the item is, in RO-Crate terms a Data Entity - that has @type File or Dataset or it starts with # then leave it as-is. - else prepend # to the @id

    • for each value of a property that starts and ends with double quotes: - If the value matches a known @id then add a reference {"@id": "#someid"} - else if the value (without quotes) matches a known name add a reference to the item with that name - else if the value (without quotes) does not start with # prepend # and see if it matches a known @id - if it does add it as a reference

    Keywords

    none

    Install

    npm i ro-crate-excel

    DownloadsWeekly Downloads

    4

    Version

    1.0.10

    License

    GPL-3.0

    Unpacked Size

    10.6 MB

    Total Files

    224

    Last publish

    Collaborators

    • ptsefton