Given that I'm not the only user of the processing scripts, and most of them do not know computer technology very well, it is necessary to make the human interaction process user-friendly.

This page has three parts: the idea, sample run, and auxiliary scripts.

The Idea

In order to minimize code-level modifications, most scripts take parameters from the command line while running. Since most of the users are not professionals in computer technology, it is unlikely that they can feed the right parameter(s) to the script via the command line. Therefore, I have created a master wrapper "start_operation.py" to guide them for each operation. If any operation is selected, the wrapper will invoke the necessary script with proper parameters.

Reducing Parameters

Since we usually process files at the level of a batch of accessions, I went through the process myself and minimized the information needed while running the script. For example, while switching the download list on a remote server, the location of extracted downloading links "_url" and the remote server address needs to be provided. Each proxy node has a code from B to E (A reserved for localhost), the user only needs to provide the server code, and the rest of the parameters like server address, port, username, password, and remote location will be entered by the wrapper based on predefined values. In addition, since we usually operate in the unit of the batch of accessions for different operations, the user only needs to provide the path to the batch folder, and the script will automatically recognize the required file in that directory.

Fast yet Flexible

The pre-filled values are changed based on the provided server code and prompt the user for confirmation. If the value is correct (in most cases), the user only needs to press enter to confirm. If any of the options are incorrect, or if any location is temporarily changed, the user can simply provide the new location while confirming.

Error Tolerance

Entering the directory correctly can be a problem for a general user. Therefore, the value provided will be sanitized and validated before being passed to the next steps. In Windows, if the directory was copied directly from the address bar, the slash was usually replaced by the backslash, which could cause serious problems when storing as a string. Therefore, I made the script to sanitize the entered value first, replacing any backslash with a slash.

It is possible that users provide an incorrect value, or if the user chose the wrong option. When a value is provided, the script will first check for it's existence before continuing. In addition, for sensitive operations like replacing the download list, the script will check for any file left and warn the user. A file left in the folder usually indicates the previous download is not yet complete. If the user indeed wants to continue, the script will prompt the user to type "confirm" before continuing. 

Sample Run

Auxiliary Scripts

List of auxiliary (non-major) scripts and their purpose.

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