2023-07-05

This is Maëlle's DBGI daily open-notebook.

Today is 2023.07.05

TODO

Check discussion: https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Check Zulip

CODE

Yesterday problem was resolved as follow:

JS:

  return new Promise((resolve, reject) => {
    const nodes = [];
    let headers = [];

    repository.query(payload).then((stream) => {
      stream.on('data', (bindings) => {
        const node = {};
        for (const binding in bindings) {
          if (bindings.hasOwnProperty(binding)) {
            node[binding] = bindings[binding].value;  // use binding as id and bindings[binding].value as label
            if (!headers.includes(binding)) {
              headers.push(binding);  // add the binding to the headers if it's not already there
            }
          }
        }
        nodes.push(node);
      });
      stream.on('end', () => {
        // Resolve the promise with the graph data and the headers when the stream ends
        resolve({nodes: nodes, headers: headers});
      });

HTML:

    <% if (typeof results !== 'undefined' && results.length > 0) { %>
        <table class="table table-striped table-responsive">
            <thead>
                <tr>
                    <% headers.forEach(function(header) { %>
                        <th><%= header %></th>
                    <% }); %>
                </tr>
            </thead>
            <tbody>
                <% results.forEach(function(node) { %>
                    <tr>
                        <% headers.forEach(function(header) { %>
                            <td><%= node[header] %></td>
                        <% }); %>
                    </tr>
                <% }); %>
            </tbody>
        </table>
        <% } else { %>
        <p>No results to display</p>
        <% } %>

Query to get the link to gnps:

PREFIX enpkg: <https://enpkg.commons-lab.org/kg/>
select ?dbgi_sample ?GNPSdashboard where { 
	?extract enpkg:has_lab_process ?dbgi_sample .
    ?dbgi_sample enpkg:has_LCMS ?LCMS .
    ?LCMS enpkg:has_gnpslcms_link ?GNPSdashboard .
}

NOTES

Should meet with pma:

D'où les données doivent venir? => DBGI + LOTUS
Structure du graph => comment faire la figure? => see article
Lien GNPS => OK

=> meeting at 2pm

TODO NEXT

Important for redaction

This is Maëlle's DBGI daily open-notebook.

Important for redaction