Decompress util #244

cuducos · 2017-09-14T22:37:10Z

This PR implements rows.utils.decompress as suggested in #230. The API is:

import rows
from rows.utils import decompress

table1 = rows.import_from_csv(decompress('filename.csv.gz'))
table2 = rows.import_from_csv(decompress('filename.csv.xz'))
table3 = rows.import_from_csv(decompress('filename.csv.bz2'))

A RunTime error is raised if:

rows can't properly guess the mimetype as a known mimetype of a lzma or gzip file
rows identifies a lzma mimetype but the lzma module is not available (a lzma lib has to be available in the OS when compiling Python it self as explained here)

https://github.com/turicas/rows/issues/230\#issuecomment-328364587

turicas

Thanks for this PR! :)
I've requested some changes/questions and we can discuss about them. =)

turicas · 2017-09-16T16:35:59Z

rows/utils.py

+    lzma_mime_types = (
+        'application/x-xz',
+        'application/x-lzma'
+    )


I think mimetype detection is not needed here - we can expect the user will call this function only if she knows the file is compressed and in one of the supported algorithms; we can do this detection automatically on the command-line interface using file-magic and then pass the correct arguments to decompress. Do you agree?

Totally : )

turicas · 2017-09-16T16:37:14Z

rows/utils.py

@@ -297,3 +310,53 @@ def export_to_uri(table, uri, *args, **kwargs):
        raise ValueError('Plugin (export) "{}" not found'.format(plugin_name))

    return export_function(table, uri, *args, **kwargs)
+
+
+def decompress(path, **kwargs):


Could you please add an algorithm parameter to this function? It should defaults to None (if None, use file extension to define it).

turicas · 2017-09-16T16:38:26Z

rows/utils.py

+        msg = "Couldn't identify file mimetype, or lzma module isn't available"
+        raise RuntimeError(msg)
+
+    with open_compressed(path, **kwargs) as handler:


Do you think having kwargs on decompress is really needed? Could you give me an example use case?

Basically encoding. On UNIX for example I barely use it. But Windows user should always add utf-8 I was told.

turicas · 2017-09-16T16:39:17Z

tests/tests_utils.py

+
+    def setUp(self):
+        self.contents = six.b('Ahoy')
+        self.temp = tempfile.TemporaryDirectory()


All the tests are failing here. I've replaced self.tmp with self.temp (was receiving a NameError) but they still fail:

====================================================================== ERROR: test_decompress_with_bz2 (tests.tests_utils.UtilsDecompressTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/turicas/projects/rows/tests/tests_utils.py", line 99, in test_decompress_with_bz2 decompressed = rows.utils.decompress(compressed) File "/home/turicas/projects/rows/rows/utils.py", line 359, in decompress raise RuntimeError(msg) RuntimeError: Couldn't identify file mimetype, or lzma module isn't available ====================================================================== ERROR: test_decompress_with_gz (tests.tests_utils.UtilsDecompressTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/turicas/projects/rows/tests/tests_utils.py", line 107, in test_decompress_with_gz self.assertEqual(self.contents, decompressed.read()) File "/home/turicas/software/pyenv/versions/3.6.2/lib/python3.6/gzip.py", line 272, in read self._check_not_closed() File "/home/turicas/software/pyenv/versions/3.6.2/lib/python3.6/_compression.py", line 14, in _check_not_closed raise ValueError("I/O operation on closed file") ValueError: I/O operation on closed file ====================================================================== ERROR: test_decompress_with_incompatible_file (tests.tests_utils.UtilsDecompressTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/turicas/projects/rows/tests/tests_utils.py", line 126, in test_decompress_with_incompatible_file with self.assertRaises(): TypeError: assertRaises() missing 1 required positional argument: 'expected_exception' ====================================================================== ERROR: test_decompress_with_lzma (tests.tests_utils.UtilsDecompressTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/turicas/projects/rows/tests/tests_utils.py", line 112, in test_decompress_with_lzma with lzma.open(compressed) as compressed_handler: File "/home/turicas/software/pyenv/versions/3.6.2/lib/python3.6/lzma.py", line 302, in open preset=preset, filters=filters) File "/home/turicas/software/pyenv/versions/3.6.2/lib/python3.6/lzma.py", line 120, in __init__ self._fp = builtins.open(filename, mode) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpr5s7bse8/test.lzma' ====================================================================== ERROR: test_decompress_with_xz (tests.tests_utils.UtilsDecompressTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/turicas/projects/rows/tests/tests_utils.py", line 120, in test_decompress_with_xz with lzma.open(compressed) as compressed_handler: File "/home/turicas/software/pyenv/versions/3.6.2/lib/python3.6/lzma.py", line 302, in open preset=preset, filters=filters) File "/home/turicas/software/pyenv/versions/3.6.2/lib/python3.6/lzma.py", line 120, in __init__ self._fp = builtins.open(filename, mode) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpz5l7xm1q/test.gz' ---------------------------------------------------------------------- Ran 184 tests in 0.848s

Are the tests passing in your machine?

turicas · 2017-09-16T16:41:44Z

rows/utils.py

+    kwargs are passed to either `bz2.openn`, `gzip.open` or `lzma.open`.
+    :param path: (str) path to a bz2, gzip or lzma file
+    """
+    filename = os.path.basename(path)


As the current API accepts filenames or file-objects,
this function should also do (this decision was inspired in the Python stdlib modules, such as csv). You can get some help using rows.plugins.utils.get_filename_and_fobj.

That was indeed pretty helpful, thanks ; )

turicas · 2017-09-16T16:42:34Z

rows/utils.py

+        raise RuntimeError(msg)
+
+    with open_compressed(path, **kwargs) as handler:
+        return handler


It's very important to ensure the file object returned is open in binary mode (so the plugins will decode the data using the desired encoding). Could you please add a test for this case?

cuducos · 2017-10-15T13:37:55Z

Ok, sorry I took too long to get back to this PR. Life's got hectic around here.

Anyway, I addressed many issues in this refactor:

made it work with file object
dumped that complexity of detecting mimetype
fixed tests
implemented the algorithm argument
ensures the output is always byte string

About tests: I've just ran python -m unittest tests/tests_utils.py so not sure if is tehre any Python 2 details I might have missed (ie wasn't able to test with tox).

Do you prefer to implement compress in this same PR or leave it to a separate one?

cuducos added 4 commits July 5, 2017 19:16

Proposal: API for rows.utils.decompress in the form of tests

48293bf

Remove proposed zip API

d62ba69

https://github.com/turicas/rows/issues/230\#issuecomment-328364587

Implement rows.utils.decompress for lzma and gzip

78338cf

Implement rows.utils.decompress for bz2

ac3bdbf

cuducos changed the title ~~Cuducos decompress~~ Decompress util Sep 14, 2017

Properly document bz2 in docstrings

f0b786d

turicas requested changes Sep 16, 2017

View reviewed changes

cuducos added 2 commits October 15, 2017 11:30

Refactor decompress function

758c1b6

Merge branch 'develop' into cuducos-decompress

837737c

turicas force-pushed the develop branch 2 times, most recently from fa144f0 to bbb2c57 Compare November 30, 2018 01:34

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Decompress util #244

Decompress util #244

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cuducos commented Oct 15, 2017 •

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cuducos commented Oct 15, 2017 • edited Loading

cuducos commented Oct 15, 2017 •

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