Error when loading csv on mysql using Python and odo module

Question

I decided to try odo for handling my csv data because it supposedly is way faster than doing it with pandas, but I can't make it work.

This is their documentation about migrating a 30gb csv file to a MySQL database:

In [1]: %time t = odo('all.csv', 'mysql+pymysql://localhost/test::nyc')
CPU times: user 1.32 s, sys: 304 ms, total: 1.63 s
Wall time: 20min 49s

I tried the same in my local MySQL instance on my OS X El Capitan but it gives me the following error:

/Library/Python/2.7/site-packages/PyMySQL-0.7.1-py2.7.egg/pymysql/err.pyc in _check_mysql_exception(errinfo)
    113 
    114     # couldn't find the right error number
--> 115     raise InternalError(errno, errorvalue)
    116 
    117 

InternalError: (pymysql.err.InternalError) (13, u"Can't get stat of '/path/to/test.csv' (Errcode: 13 - Permission denied)") [SQL: u'LOAD DATA  INFILE %(path)s\n            INTO TABLE test_file2\n            CHARACTER SET %(encoding)s\n            FIELDS\n                TERMINATED BY %(delimiter)s\n                ENCLOSED BY %(quotechar)s\n                ESCAPED BY %(escapechar)s\n            LINES TERMINATED BY %(lineterminator)s\n            IGNORE %(skiprows)s LINES\n            '] [parameters: {'escapechar': '\\', 'encoding': 'utf8', 'skiprows': 1, 'delimiter': ',', 'lineterminator': u'\n', 'quotechar': '"', 'path': '/path/to/test.csv'}]

At first, I thought it was an error with file permissions, but then I discovered that the table is created successfully and with the right column names, so odo is able to access the file. So, I don't really understand the error (13, u"Can't get stat of '/path/to/test.csv' (Errcode: 13 - Permission denied)")

What else can I check?

File system level permissions. Error 13 indicates issues on the file system level. You may not have access to the csv file itself. — Shadow
– Shadow, Commented Jun 7, 2016 at 21:06
Well, I know that I have access. Like I said on the post, odo actually creates the table with the column names present on the csv. The problem might be that MySQL can't access that file, but I already changed it's permissions to 777 and the parents folders have at least "read" permission — estemendoza
– estemendoza, Commented Jun 7, 2016 at 21:35

estemendoza · Accepted Answer · 2016-06-07 22:12:58Z

0

Well, it was because MySQL couldn't access the file. It seems that it needs to be inside the mysql installation folder, which in my case was /usr/local/mysql-5.6.20-osx10.7-x86_64/.

I tried to put it inside the data folder, /usr/local/mysql-5.6.20-osx10.7-x86_64/data/my_db and that didn't work out.

answered Jun 7, 2016 at 22:12

estemendoza

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