我应该为MySQL数据库插入程序使用python类吗？

Question

I have created a database to store NGS sequencing results. It consists of 17 tables to store all of the information. The results are stored in spreadsheets which I parse data from and store in variables using python (2.7), and then use the python package mysqldb to insert data into the database. I mainly use functions to obtain the information i need in variables, then write a loop in which I call this function followed by a 'try:' statement to insert. Here is a simple example:

def sample_processer(file):
    my_file = open(file, 'r+')
    samples = []
    for line in my_file:
        ...get info...
        samples.append(line[0])
    return(samples)

samples = sample_processor('path/to/file')

for sample in samples:
    try:
        sql = "samsql = "INSERT IGNORE INTO sample(sample_id, diagnosis, screening) VALUES ("
        samsql = samsql + "'"+sample+"'," +sam_screen_dict.get(sample)+"')"  
    except e: 
        db.rollback()
        print("Something went wrong inserting data into the sample table: %s" %(e))

*sam_screen_dict is a dictionary i made from another function.

This is a simple table that I upload into but many of them call of different dictionaries to make sure the correct results are uploaded. However I was wondering whether there would be a more robust way in which to do this using a class.

For example, my sample_id has an associated screening attribute in the sample table, so this is easy to do with one dictionary. I have more complex junction tables, such as the table in which the sample_id, experiment_id and found mutation are stored, alongside other data, would it be a good idea to create a class for this table, calling on a simple 'sample' class to inherit from? That way I would always know that the results being inserted will be for the correct sample/experiment etc.

Also, using classes could I write rules for each attribute so that if the source spreadsheet is for some reason incorrect, it will not insert into the database? Ie: sample_id is in the format A123/16. Therefore using a class it will check that the first character is 'A' and that sample_id[-3] should always == '/'. I know I could write these into functions, but I feel like it would take up so much space and time writing so many 'if' statements, that if it is stored once in a class then this would be alot better.

Has anybody done anything similar using classes to pass through their variables to test that they are correct before it gets to the insert stage and an error is created?

I am new to python classes and understand the basics, still trying to get to grips with them so a point in the right direction would be great - as would any help on how to go about actually writing the code for a python class that would be used to make a more robust database insertion program.

Answer 1

17tables it means you may use about 17 classes. Use a simple script. webpy.db https://github.com/webpy/webpy/blob/master/web/db.py just modify few code. Then you can use webpy api: http://webpy.org/docs/0.3/api#web.db to finish your job.

Hope it's useful for you