State of the Project (Week 4)


  • (With assistance,) finally determined the cause of the problems I had been having with my local Phylet (the visualization space was empty). Turned out that the Python package py2neo had gotten a major facelift and hadn’t been working as it should. Some problems with the d3 and bootstrap js files were slap-dash corrected.
    1.  In, graph_db.get_node() was changed to graph_db.node().
    2. In, my_node.get_related_nodes() was changed to graph_db.match() (note the change from my_node to graph_db). match() also takes different arguments. Py2neo’s .get_properties() is unchanged.
    3. In, the lines adding py2neo to the system path were commented out, as they referred to an old py2neo package and I had it added to my path already. [NEEDS: a more permanent solution.]
    4. In index.html, replaced all <script> pointing back to d3 with a <script> pointing directly to d3.v3.min.js, which is the full d3 min code that I downloaded to my computer. [NEEDS: to refer back to web-based d3, so users don’t have to download?]
    5. In index.html, removed a broken (404) script – bootstrap-popover.js. [NEEDS: a working replacement. A quick attempt at a local copy didn’t work – probably wasn’t even the same script.]
  • Finished drafts of annotations on index.html and – annotations for gol.js have already been completed. Created a simplified function map for how the three pieces work together.
  • Installed Neo4j and Phylet on Ubuntu partition, to flesh out the notes for Linux installation in the tutorial.
  • Defined current obstacle in getting a fully functional visualization. This is what the viz looks like now: little-vizThe blue nodes are “root nodes,” meaning they are unresponsive. Phylet is not getting fed the keys child_count and parent_count correctly – they revert to the default value, 0. By replacing 0 with 10 and 2, respectively (randomly chosen values), the viz becomes responsive and I can expand nodes to show children. Of course, this doesn’t actually solve the problem, but it seems to confirm that this is where the problem lays. Clicking on the node “life” produces this, which is an improvement but still slightly… cluttered:

To do:

  • Push edits back to repo on bitbucket.
  • Start work on fleshing out the website.
  • Finish tutorials (up to point I am now).
  • Make the database data we are using available for download.
  • If Phylet becomes fully functional: begin applying alternate visualizations.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s