Workspace Structure

The WE1S Workspace is a cloud of virtual computers with all the resources you will require to manage your workflow. Most of your work will be on the write volume, which we will generally refer to as the Workspace. Technically, however, the Workspace also includes other volumes, such as the MongoDB instance described below. Each volume has access to the same data files.

This section provides a brief overview of what you will see when you launch the Workspace. An outline of the over structure is displayed below, followed by explanations of each component.

write
┣ getting_started
┣ project_template
┣ create_template_archive.ipynb
┣ getting_started.html
┣ mongo_express.html
┣ new_project.ipynb
┣ template_package.py
┗ README.md

The write Folder

The write folder is the location where you will do most of your work. When you launch the Workspace, you will see five files and two folders located inside your write folder. The functions of each of these is described below.

getting_started.html

This is simply a convenient file that you can open to launch this Getting Started guide. It actually just redirects the browser to getting_started/index.html. It is a read-only file and cannot be modified.

README.md

This is a Markdown file containing information about the version of the project template in your Workspace. If you download a later version, it may no longer be compatible, and you may have to install the most recent version of the Workspace. The information in this file can therefore be useful to check whether your project template and your Workspace container are compatible. The README.md file is a read-only file and cannot be edited.

template_package.py

This is Python script that contains functions used by both the create_template_archive and new_project notebooks. It is a read-only file and cannot be edited.

create_template_archive.ipynb

This notebook can be used to make a compressed .tar.gz file of your project_template folder. Generally, you will only want to do this if you have customized the template and wish to use your customizations in another project. Use this notebook to create an archive of your custom template, and you can point to it as your template source when creating projects with the new_project notebook.

new_project.ipynb

This notebook is the main starting point for you workflow. Use the new_project notebook to create a new copy of the project_template folder with metadata about your specific project. You can then enter the new project folder to import your data into the new project.

getting_started

This folder contains the Getting Started web site you are currently reading. The site can be launched by going to getting_stared/index.html or by launching getting_started.html from the Workspace write folder. You should not need to modify anything in this folder, unless you want to use the Getting Started site as a place to add notes to yourself in the site's individual web pages.

project_template

This folder contains are the files and resources required for the individual modules in WE1S Workspace. When a new project is created, these resources are copied from the project_template folder into the new project folder and become available for use in the new project.

MongoDB

The Workspace comes packaged with an instance of the MongoDB database, running on mongodb://mongo:27017. You can use this the MongoDB instance to manage your data. MongoDB stores data in json-like records similar to the json files used in Workspace projects, making the interchange of data between the two relatively transparent. Modules access MongoDB databases through Python's pymongo wrapper. The use of MongoDB is optional. You can also choose to import your data from flat files.

If you wish to use MongoDB, the mongo-express.html file will launch MongoExpress, a web-based admin interface for MongoDB, running on port 8081. This will allow you to perform some database administration tasks without running Python code.

To Do

What other information might be useful here?