map2model is no longer used by Bioschemas for generating web representations of the specifications. The functionality is now provided by GoWeb.

This repository is now being archived.

Bioschemas.org map2model

map2model is a Python module that facilitates Bioschemas Groups in the specification definition process.

map2model retrieves properties and Bioschemas fields (Marginality, Cardinality and Controlled Vocabularies) from Bioschemas mapping files (in GDrive), then classifies properties into two groups:

1. Extended properties: Properties that are part of the extended schema.org Type.
2. New properties: Properties that are new to the schema.org vocabulary or are completely new to schema.org.

After classifying the properties, map2model generates a Markdown file that can be interpreted by Bioschemas.org's web site thereby updating the Bioschemas.org web pages.

Comments on each specification should be done through the GitHub issues tool within the bioschemas repository. This enables tracking, commenting on and executing of corrections.

If you want to modify the Flow Chart Click here and store the result in the doc > img folder with the name map2model_workflow.jpg.

Run map2model on your computer

Requirements

Before starting, please ensure you have the following installed:

1. Git https://git-scm.com/downloads
2. Python 3 https://www.python.org/downloads/
3. Pip https://pip.pypa.io/en/stable/installing/

Executing map2model

1. Clone the map2model repository: git clone https://github.com/BioSchemas/map2model.git
2. Add the Bioschemas GDrive Folder to your Google Account Drive.

   In your Google Drive Account go to Shared with me, right click the Bioschemas.org folder and select Add to my Drive)

3. Open the Terminal or Console application of your Operating System and go to the folder where you cloned the map2model repository.
4. Modify the spec2model > configuration.yml file in your cloned repository (configuration.yml tells map2model which specifications exist and where information on them can be found).

   If you need help to modify the configuration.yml file, please refer to the Adding new specifications section later in this readme.

5. Install Python dependencies using the command pip3 install -r requirements.txt.
6. Run the map2model module by executing the command python3 run.py.
7. After executing the run.py command a web browser will ask for a Google Account authentication. Log in using the account you used for step 2.
8. Once complete, the specifications can be found in a subfolder inside map2model > docs > spec_files folder. There should be a folder for each specification listed in configuration.yml.

Update specifications repository

1. Fork Bioschemas specification repository
2. Clone your fork to your local computer.
3. If you added a new specification, copy the entire folder from map2model > docs > spec_files into the top level of the local copy of specifications.
4. If you changed an existing specification copy the specification.html file from the specification subfolder in map2model > docs > spec_files into the appropriate specification folder in the local specifications repo.
5. Check everything is OK. If it is, commit your changes. Then push to the GitHub hosted version of your fork.
6. Make a Pull Request of your specifications repository fork:
   • Go to the GitHub webpage and choose your fork of the main specifications repository.
   • Click the button called Create new pull request
   • Click the green button titled Create pull request
   • Write a simple summary of your changes in the Write window.
   • Click the Create pull request button
7. Your changes will now be manually checked to ensure they do not conflict with existing content.
8. Wait until your Pull Request is merged into Bioschemas Web

   To preserve Bioschemas Web Page, changes to bioschemas.github.io repository will be issued by Bioschemas Web Master.

9. Check your changes at Specifications Bioschemas Web section

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Advanced user's documentation

Adding new specifications

If you have created a new specification (or a specification is missing from the map2model > docs > specification_md_files folder) you will need to extend the map2model > spec2model > configuration.yml file.

If you are unfamiliar with yaml, please read http://yaml.org/.

1. Open the map2model > spec2model > configuration.yml file.
2. Erase all the file content and start the .yml file with

specifications:

1. Add the following yaml structure per each specification:

  - name :
    g_folder:
    g_mapping_file:
    status: revision
    spec_type: Profile
    use_cases_url:
    version: 0.0.1

  - Please be careful with spacing, as it is important in YAML!

1. Apart from use_case_url all fields must have a value:
   • name is the name of the specification
   • g_folder is the name of the gDocs folder in which the new specification exists. E.g., a Tool specification will be found in the Tool folder (i.e., gDrive > BioSchemas.org > Specifications > Tool).
   • g_mapping_file : in the g_folder you should have a mapping file based on the original template. Write the name of the mapping file here, e.g., Tool Mapping.
   • use_cases_url : in the g_folder you may have a use case document. If it exists, paste a link to it here.
2. Re-run python3 run.py. Your new markdown files should be in the bioschemas-map2model > docs > specification_md_files folder.

Create your own client_secrets.json

map2model can work with the generic client_secrets file, but here you have the process to create your own json. It is unlikely you will ever need to do this, but the instructions remain for completeness.

Create a new Google's APIs Project and add Google Drive API Client:

• Go to Google's APIs Console and create your own project. Call it whatever you want.
• You will need to wait for a few moments while Google creates the project. Refresh the page and you should see your new project listed.
• Click on the Google APIs logo (top left of screen). If you have existing projects, select the new one in the dropdown box next to the Google APIs logo.
• Under G Suite APIs you will see Drive API. Click on it.
• On the next page, click on Enable
• You should see a yellow warning at the top of the page informing you of the need for credentials. Do not click the create credentials button at the right of this warning. Instead click the key icon in the left menu bar.
• In the new dialog box there is a dropdown called create credentials... choose OAuth client ID.
• A form with radio buttons will appear, but it is greyed out and you cannot select anything. Instead click the blue Configure consent screen button on the right.
• In the new form enter whatever product name you wish and click save.
• You will be returned to the form with radio buttons; select Web application.
• In the text box called 'Authorised Javascript origins' type http://localhost:8080 (notice the lack of a trailing slash)
• In the text box called 'Authorised redirect URIs' type http://localhost:8080/ (notice the trailing slash)
• Click create then OK.
• You will be on a page called 'Credentials' which has a table with the name of your new app. At the far right you will see a download icon (an arrow pointing down, above a line). Clicking on this allows you to download your credentials.
• The downloaded file will have a very long name, e.g., client_secret_896441073116-l0karljg25m6uvss45t48ufb9d7u3kku.apps.googleusercontent.com. Change the name to client_secrets.json and move it to the top level of your cloned bioschemas-map2model repository.