Overall Directory Structure


The main python package containing all the python code. filename conventions include:

  • view.py: Server side code for displaying the various GUI data grids
  • forms.py: Server side code for displaying and responding to GUI forms

Some key subdirectories are:

  • static: Static files such as js and html files that are delivered directly to the client
  • main:
  • api_1_0: Support for the internal api between the client and the server
  • api_2_0: Support for the external http api
  • databases: SQLalchemy based definition of postgres database tables


The folder contains shell scripts, which should be run every so often (e.g. using crontab) to update and maintain the database. The two scripts run most regularly are:-

  • daily_update.sh Checks databases to see if any assemblies need to be sent or any schemes need to be called. Simply calls [update_all_schemes](Maintenance Scripts#markdown-header-update_all_schemes) and update_assemblies for the databases specified in the script. The script can be changed to add/remove databases, change priorities,job queues etc.
  • daily_import.sh Updates all databases by calling importSRA


Contains the source documents for building the documentation that appears on readthedocs


A local copy of the documentation can be built in various formats. html formatted documentation can be found in _build/html subdirectory and can be viewed by opening index.html in a browser. To make the documentation first install the python virtual environment using install/createEnvironmentForDocumenationBuild.sh and then activate the entero_docs environment and within docs run

make clean
make html

It is also possible to make documentation based on code comments using sphinx-apidoc e.g.

sphinx-apidoc -f -o source ../entero ../entero/databases/* ../entero/ExtraFuncs/unidecode


Contains the log files. Info log contains general information e.g when an assembly was sent or when a user uploaded a read, whereas the error log contains information about all the exceptions thrown. The system log contains information from the any scripts that are run (see below)

Root files


The file containing scripts which run in the context of the app see flask-scripts. The scriptsavailable are documented here


A file containing all the python modules required. If extra modules are added, this file should be updated by pip freeze > requirements.txt


Contains all the required linux packages


The html sub directory contains the actual JavaScript documentation produced from the inline code comments. Just open the index.html in this folder with a browser to view the documentation. In order to update documentation jsdoc needs to be installed (npm install jsdoc). Also a bootstrap template is used (npm install ink-docstrap). In the config.json file change the template in opts to the correct location (depending on where ink-docstrap was installed).


If you want to use the default template, then just delete the template entry in the config. Any new .js files need to be added to the include entry in the config file.

"source": {

To produce the documentation just cd to the jsdoc directory and run .. code-block:: json

jsdoc -c conf.json