We (KWS SAAT SE & Co. KGaA) like your Sequenceserver very much. Unfortunately, we have several hundreds of blast databases. Using the default Sequenceserver list does not work for us.

This was the reason why I tried to implement jstree (https://www.jstree.com) and a data/folder structure to group the databases.
Because some/many of the databases might belong to different groups, we have a raw data folder where all files are located in and a Sequence server data folder with many subfolders that only include symbolic links.

To explain everything, I created a new example data structure including some randomly selected databases.

The folder structure:

The raw_data folder including the fasta and blast files:

The data folder used by the Sequenceserver only includes symbolic links:

The resulting tree shown in the Sequenceserver mimics 1:1 the folder structure. This makes it easy for everyone to define their specific tree structure. Furthermore, it is possible to use the search field next to e.g. ‘Nucleotide databases’:

I forked your project and created a new branch ‘tree’. See https://github.com/bjoern-hammesfahr/sequenceserver/tree/tree

Unfortunately, I do not know React and my time was limited. Furthermore, I did not want to introduce to many changes, therefore I hide your database list and simulate a selection when a db gets selected in the tree.

Maybe this idea is helpful for you and it would be possible to implement it to the Sequenceserver.

My changes:

• package.json: add jstree (line 35)
• public/config.json: add jstree (line 30)
• public/vendor: automatically changed?
• public/js/search.js
  • add jstree (line 4)
  • add key tree to getInitialState (line 210)
  • add data['tree'] to setStage (line 230)
  • add timeout that clicks the hstree:div after 1s (line 241:244)
  • add tree={this.state.tree} to Databases (line 344)
  • add function handleLoadTree to load the tree (line 687:729)
  • add id database_list to div panel panel-default (line 770)
  • add this.renderDatabaseSearch(category) to add the nucleotide/protein searches (line 773:775)
  • hide the button (line 776) and the ul (line 781) because of time and to reduce the number of changes
  • add this.renderDatabaseTree(category) to add the nucleotide/protein trees (line 793:795)
  • add function renderDatabaseSearch to render the search (line 800:814)
  • add function renderDatabaseTree to render the tree (line 816:833)
• public/css/sequenceserver.css: add jstree (line 8)
• lib/sequenceserver/database.rb
  • add categories to Database stucture (line 22)
  • add method tree to prepare the tree data (line 105:125)
  • determine_formatted_fastas: change line.split(' ') to line.split("\t"), because this did not work for us (line 122)
  • determine_formatted_fastas: add get_categories (line 124)
  • add method get_categories to get the category for each fasta db (line 281:285)
• lib/sequenceserver/routes.rb: add tree to searchdata.json (line 79)