Directory Structure

│   │
│   └───ms_tree
│         enterobase_generic_tree.html
│         MSTree_holder.html*
│         PhyloTree_holder.html
    │    │
    │    └───ms_tree
    │    │     base_tree.js*
    │    │     d3_m_tree.js*
    │    │     d3_p_tree.js
    │    │     grid.js*
    │    │     context.js*
    │    │
    │    └───SlickGrid

(files with an asterix need to synched with the standalone version of GrapeTree)

There are two trees phylogenetic (SNP) and MS (GrapeTree), both inherit from the same class D3BaseTree (in base_tree.js) To display the trees the following urls can be used:-

  • enterobase_root/ms_tree/tree_id or enterobase_root/ms_tree?tree_id=*tree_id*
  • enterobase_root/phylo_tree/tree_id or enterobase_root/phylo_tree/tree_id

The urls are specified in main/views and all call the generic method generate_tree_page in the entero/main/views module . This method obtains information about the tree, checks the user has permission (if a non-public tree) and renders the template. Different templates are rendered depending on the tree type, MSTree_holder.html and PhyloTree_holder.html. Both include shared functionality in Enterobase_generic_tree.html (see below)

Integration of Grape Tree with Stand Alone Version

In order to to integrate the stand alone and Enterobase versions of GrapeTree, the file structure and architecture of Grape Tree in Enterobase is slightly complicated. In entero/templates/ms_tree is MSTree_Holder.html, which is the same as the standalone version and any changes in this file will effect both. Similarly in* entero/static/js/tree* , the following files have to be synched with the stand alone version

  • base_tree.js
  • d3_m_tree.js
  • help.js
  • grid.js
  • context.js

Also entero/static/css/grapetree.css also needs to be synched

MS_Tree_holder.html contains the following lines, thus ensuring enterobase_generic_tree.html will only be included in the web version

{% if tree_id%}
{% include 'ms_tree/enterobase_generic_tree.html' %}
{%endif %}

entero_base_generic_tree.html contains code specific to the enterobase version and will attempt to load the tree whose id was supplied by flask (in the variable tree_id). In this file, the method processEnteroData will process the data obtained from enterobase e.g. convert legacy data, combine layout and actual data. This data is then passed to the generic loadMSTree function in MSTree_holder.html

Tree Data

Trees are stored in user_preferences and manipulated via Analysis Objects like any other Analysis Types. Trees are stored in three files data.json, layout.json and a nwk file. The location of these files are specified in the objects data, but are generally located in

  • data_file The location of the file containing json data in the following format
    • isolates A list of the metadata for each strain. Each item in the list consists of a dictionary of key/value pairs, with ‘StrainID’ being the strain id in the database and ID being the node ID that the strain is associated with. For legacy trees, this will be ST, but in more modern trees (which have node data specified in a nwk file, ID is the be assembly barcode , which are the identifiers used in the nwk file e.g


  • metadata_options A dictionary of fields to information about that field
    • label The only parameter required - the human readable label
    • category The type of field. For Enterobase data this can be one of four values
      • Custom - the field mirrors a custom column in Enterobase
      • User Added - a column added by the user that is specific to the tree
      • Metadata - standard metadata from Enterobase
      • Experiment - a column from experiment or scheme data
    • coltype - the type of data e.g. character or number
    • grouptype - how the categories are ordered e.g size alphabetical
    • colorscheme - either category or gradient
  • current_metadata The name of the metadata last displayed in the tree
  • layout_file The location of the file containing the layout information of the tree
    • node_positions A dictionary of node id to an array of x,y co-ordinates e.g {“ST232”:[762,232],”ST233”:[22,33],…}
    • display_category The category currently displayed
    • nodes_links Extra information about the nodes/links:
      • max_link_scale
      • max_link_length
      • base_node_size
      • size_power
      • scale
      • translate
      • link_font_size
      • show_link_labels
      • show_node_labels
      • node_font_size
      • custom_colors
      • hide_link_length
      • show_individual_segments
      • node_collapsed_value
      • node_text_value
      • manual_collapsing
      • square_root_scale
  • nwk_file the nwk file containing information for the node layout. The identifiers in the nwk file are assembly barcodes