The use of from rosetta.txt.api import * inside tests has created dependencies that break tests. This import * statement makes it so every test depends on every import statement in the rosetta api. Since MySQLdb doesn't import for me (after 10 minutes of setting it up it still doesn't), and docx has issues that prevents it from working for many people, I can no longer run tests for anything.

It would be safer to import only what is needed. Also, since things like docx and mysql are problematic and/or difficult to fully install, it might make sense to protect these imports like in this pull request.

Following the example in https://github.com/columbia-applied-data-science/rosetta/blob/master/examples/vw_helpers.md

There is an error when I run LDAResults() the following error prints:

ImportError Traceback (most recent call last) in () 3 lda = LDAResults('C:\Users\Desktop\DATA\LDA\topics.dat', 4 'C:\Users\Desktop\DATA\LDA\predictions.dat', 'C:/Users/Desktop/DATA/LDA' + '/sff_basic.pkl', ----> 5 num_topics=num_topics) 6 lda.print_topics()

C:\Anaconda\lib\site-packages\rosetta\text\vw_helpers.pyc in init(self, topics_file, predictions_file, sfile_filter, num_topics, alpha, verbose) 230 231 if not isinstance(sfile_filter, text_processors.SFileFilter): --> 232 sfile_filter = text_processors.SFileFilter.load(sfile_filter) 233 234 self.sfile_frame = sfile_filter.to_frame()

C:\Anaconda\lib\site-packages\rosetta\common_abc.pyc in load(cls, loadfile) 40 """ 41 with smart_open(loadfile, 'rb') as f: ---> 42 return cPickle.load(f)

ImportError: No module named text_processors

I think I hit on the major points and recommendations I've gotten (but yell at me if I forgot any!). I changed it so that the filtering is done updating the original dict as much as possible and I made it clear in the documentation that that's the idea. I added back in the _done_check() method's functionality that I previously removed. I also wrote a couple tests.

So this is probably (at least from my perspective) pretty close to being mergable. Let me know what you guys think!

Hi guys,

I'm working with word_tokenize, and it doesn't handle acronyms with dots very nicely. For example in the sentence "The U.S. official said", we get 'U' and 'S' as separate tokens. I could imagine we'd replace the the line:

text = re.sub(r'(?:\s|\[|\]|\(|\)|\{|\}|\.|;|,|:|\n|\r|\?|\!)', r'  ', text)

by:

text = re.sub(r'(?:\s|\[|\]|\(|\)|\{|\}|;|,|:|\n|\r|\?|\!)', r'  ', text)
text = text.replace('.', '')

That is, omit the period from the first replacement, and put it in the second line. Any comments? Thank you! David

cleaned up changes to vw_helpers.py to hide tokenset per Ian's comments

sped up LDAResults.predict by ~5x. Renamed 'cmd' module to 'cmdutils' to avoid conflict with native python 'cmd'. I don't know how you guys feel about pull requests, but I think these changes would be useful for others. Thanks for letting me use your code. -Louis

Hey guys,

I was curious about how to interpret output from the prob_token_topic function. I noticed that the probability outcome changes depending on the number of topics being conditioned on.

The probability of 'kennedy' in topic 0 will be different under the following: lda.prob_token_topic(token='kennedy', c_topic=['topic_0']) lda.prob_token_topic(token='kennedy', c_topic=['topic_0', 'topic_3'])

Is this as expected? How should these outcomes be interpreted?

This is in reference to the following issue: https://github.com/columbia-applied-data-science/rosetta/issues/21

I wrote a class called SqliteDBStreamer which is intended to mirror the usage of TextFileStreamer except instead of having a folder of text files as the main source of data, the files are kept in a sqlite3 database which makes many standard file operations much faster.

I personally think this is NOT READY to merge. Each time I look at it, I find little weird things left-over from how I was using the code a month ago (when I basically just hacked it together). But I wanted to throw it up here in case you guys see something really bazaar. I tried to make it as much like TextFileStreamer as possible. In the info_stream, for example, I do not currently have fields like "modification_date". I could add that as a trigger to the sqlitedb file, but I wasn't sure how necessary it was. I also have a few tweaks I need to add that speed this up, but those are minor details aside from the overall setup.

At this point, I'm basically only treating the sqlitedb as a never-changing object (i.e. add files once and then leave them there). Now this probably doesn't make sense (though I've personally not yet had any other use case), but I'm still thinking the best way to deal with those problems. In it's current state basically all sqlite details are hidden, which is pretty nice at the moment.

Anyway I imagine myself making many changes to this, but I figured I might as well throw this up here so you guys can give me some feedback if I'm doing something really stupid. Also I have an analysis that I'm doing for declass which could be used as a guide for using these classes, but I need to adapt it to this newer code (though on the surface it looks basically identical to how it's done with TextFileStreamer). Once I do that it could be good documentation.

This would be a breaking change since it separates text.streamers from text.database_streamers. The difference is that people can use rosetta.text without having to have database dependencies like pymongo and MySQL-python (the latter of which requires a mysql client dependency, which is kind of annoying to carry around if you aren't using mysql). This would partially address people's install issues (e.g. https://github.com/columbia-applied-data-science/rosetta/issues/48)

The other changes are so that rosetta installs using into python3 environments. There are a couple slightly dirty solutions here, implemented by catching ImportError, but for the most part rosetta is python3 compatible so it might as well work there.

Both parse_lda_topics() and parse_lda_predictions() were painfully slow. Most (~90%) of this was due to unnecessary formatting and re-casting on every iteration.

Speedups on this branch, using

time python lda_sums_test.py

in terminal are the following:

for a 1mil row predictions.dat file (200k unique doc ids from vw lda run 5 passes, 10 topics) current branch running

import rosetta.text.vw_helpers as ros_vw_h

predictions_file = '/tmp/prediction_large.dat'

num_topics=10

start_line = ros_vw_h.find_start_line_lda_predictions(predictions_file, num_topics)
pred_iter = ros_vw_h.parse_lda_predictions(predictions_file, num_topics, start_line, normalize=False,
                                                                       get_iter=False)

gets

real    0m5.092s
user    0m4.628s
sys 0m0.465s

vs

real    10m49.159s
user    10m46.165s
sys 0m2.182s

on the master branch. (Note: the fine_start_line() wasn't altered between branches and is relatively fast compared to the parser, i.e. ~1.5s)

for a 30k row topics.dat file (same lda run as above) current branch running

import rosetta.text.vw_helpers as ros_vw_h

topics_file = '/tmp/topics_large.dat'

topics_iter = ros_vw_h.parse_lda_topics(topics_file, num_topics,
                                                                  normalize=False, get_iter=False)

get

real    0m1.461s
user    0m1.219s
sys 0m0.248s

vs

real    1m48.375s
user    1m47.796s
sys 0m0.505s

on the master branch.

You can run kernprof to see line by line profile comparisons. The differences overall are quite significant in both time and cpu load....

Aside: due to a name/indexing bug in pandas 0.16.2+ which is not going to be fixed until 0.17 some tests started failing after a latest update. Probably the best for now is to simply ignore the name check in assert_series_equal in tests; this doesn't alter the validity of the tests in question.

Some cleanup:

• removed redundant probability data frame in LDAResults * cleaned up and made more uniform
• removed catdoc from list of unix file converter utils since it's no longer supported and fails on OSX; replaced it with antiword utility
• test cleanup to reflect above

Parsing the lda topics file, i.e. --readable_model output of a vw lda run, parsed the entire file into memory ignoring the fact that possible many of the tokens are "garbage," i.e. not included in the set of user provided tokens (hashes). This forced classes like (LDAResults)[https://github.com/columbia-applied-data-science/rosetta/blob/vwresults/rosetta/text/vw_helpers.py#L205] to load more data than necessary into memory. The following PR adds

    * a max token hash number argument to (parse_lda_topics)[https://github.com/columbia-applied-data-science/rosetta/blob/vwresults/rosetta/text/vw_helpers.py#L205]. 
    * checks first for a max token hash number coming from (s_file_filter)[https://github.com/columbia-applied-data-science/rosetta/blob/vwresults/rosetta/text/vw_helpers.py#L239] in LDAResults 

The README file lists out some dependencies, but excludes NLTK. Without NLTK, I cannot import Rosetta, see below. Is there any way to load Rosetta without installing NLTK (as I really just wanted to look at the parallel API)? If not, it should be documented.

Thanks!

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-4-03c43361a895> in <module>()
----> 1 import rosetta.parallel

/usr/local/lib/python3.5/dist-packages/rosetta/__init__.py in <module>()
----> 1 from rosetta.text.api import *

/usr/local/lib/python3.5/dist-packages/rosetta/text/api.py in <module>()
----> 1 from rosetta.text.streamers import TextFileStreamer
      2 
      3 from rosetta.text.text_processors import \
      4     TokenizerBasic, MakeTokenizer, SFileFilter, VWFormatter
      5 

/usr/local/lib/python3.5/dist-packages/rosetta/text/streamers.py in <module>()
     15 from .. import common
     16 from ..common import lazyprop, smart_open, DocIDError
---> 17 from . import filefilter, text_processors
     18 
     19 

/usr/local/lib/python3.5/dist-packages/rosetta/text/text_processors.py in <module>()
     22 import math
     23 
---> 24 import nltk
     25 import numpy as np
     26 import pandas as pd

ImportError: No module named 'nltk'

I am trying to run LDA in VW using Rosetta. It seems to be working fine for smaller number of topics but as soon as I go to 50 or 100, step 3: read the results with LDAResults fails => I get a "Killed" error. I don't think this is a memory problem because I am running my code on a robust machine with 50GB of RAM. What's going on? Is this a VW or Rosetta issue? How can I solve it? Thanks!

Once I have doc_tokens.vw, this is what I am running in order: Step 1: `from rosetta.text.text_processors import SFileFilter, VWFormatter sff = SFileFilter(VWFormatter()) sff.load_sfile('doc_tokens.vw')

df = sff.to_frame() df.head() df.describe()

sff.filter_extremes(doc_freq_min=500, doc_fraction_max=0.8) sff.compactify() sff.save('sff_file.pkl')`

Step 2: rm -f *cache vw --lda 100 --lda_alpha 0.1 --lda_rho 0.1 --cache_file ddrs.cache --passes 10 -p prediction.dat --readable_model topics.dat --bit_precision 16 doc_tokens_filtered.vw

Step 3: from rosetta.text.vw_helpers import LDAResults num_topics = 5 lda = LDAResults('topics.dat', 'prediction.dat', 'sff_file.pkl', num_topics=num_topics) lda.print_topics()

My vw data is of this format

| this is great
| I try to learn English everyday
[...]

saved as data.vw I try to run this code:

from rosetta.text.vw_helpers import LDAResults
from rosetta.text.text_processors import SFileFilter, VWFormatter

def generate_filefilter():
    sff = SFileFilter(VWFormatter())
    sff.load_sfile('data.lda.vw')

    df = sff.to_frame()
    df.head()
    df.describe()

    sff.filter_extremes(doc_freq_min=5, doc_fraction_max=0.8)
    sff.compactify()
    sff.save('sff_file.pkl')

if __name__ == '__main__':
    generate_filefilter()

And the error is:

Traceback (most recent call last):
  File "/<home>/.venv/lib/python2.7/site-packages/rosetta/text/text_processors.py", line 380, in _parse_preamble
    if preamble[-1] != ' ':
IndexError: string index out of range

I installed rosetta, and tried the run examples/plot_classifiers.py - got:

/usr/local/lib/python3.4/site-packages/rosetta/text/streamers.py in <module>()
     10 import os
     11 from scipy import sparse
---> 12 import MySQLdb
     13 import MySQLdb.cursors
     14 import pymongo

ImportError: No module named 'MySQLdb'

^ This isn't listed as a dependency on the readme. Should it be ? Futhermore, it wasn't installed when I used pip to install rosetta.

>>> import rosetta
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "rosetta/__init__.py", line 1, in <module>
    from rosetta.text.api import *
  File "rosetta/text/api.py", line 1, in <module>
    from rosetta.text.streamers import TextFileStreamer
  File "rosetta/text/streamers.py", line 20, in <module>
    import pymongo
ImportError: No module named pymongo

Pymongo too.

>>> import rosetta
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/aljohnson/code/rosetta/rosetta/__init__.py", line 1, in <module>
    from rosetta.text.api import *
  File "/Users/aljohnson/code/rosetta/rosetta/text/api.py", line 1, in <module>
    from rosetta.text.streamers import TextFileStreamer
  File "/Users/aljohnson/code/rosetta/rosetta/text/streamers.py", line 22, in <module>
    from rosetta.parallel.parallel_easy import imap_easy, parallel_apply
  File "/Users/aljohnson/code/rosetta/rosetta/parallel/parallel_easy.py", line 13, in <module>
    import cPickle
ImportError: No module named 'cPickle'

cPickle too...

The weird thing... is that I'm seeing all these listed in the requirements.txt. So at this point I'm like wtf I'm just going to use virtual env.

[email protected] :
~/code/rosetta
$ virtualenv -p `which python` rosetta_env/ 
Running virtualenv with interpreter /usr/bin/python
New python executable in rosetta_env/bin/python
Installing setuptools, pip, wheel...done.
[email protected] :
~/code/rosetta
$ source rosetta_env/bin/activate
(rosetta_env)
[email protected] :
~/code/rosetta
$ ls
CONTRIBUTING.md  MANIFEST.in      README_data.md   examples         notebooks        requirements.txt rosetta_env      setup.py
LICENSE.txt      README.md        docs             makefile         notes            rosetta          scripts
(rosetta_env)
[email protected] :
~/code/rosetta
$ pip install -r requirements.txt 
/Users/aljohnson/code/rosetta/rosetta_env/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
Collecting pandas (from -r requirements.txt (line 1))
/Users/aljohnson/code/rosetta/rosetta_env/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
  Downloading pandas-0.16.2-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (7.3MB)
    100% |████████████████████████████████| 7.3MB 77kB/s 
Collecting scikit-learn (from -r requirements.txt (line 2))
  Downloading scikit_learn-0.16.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (5.4MB)
    100% |████████████████████████████████| 5.4MB 106kB/s 
Collecting statsmodels (from -r requirements.txt (line 3))
  Downloading statsmodels-0.6.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.0MB)
    100% |████████████████████████████████| 4.0MB 73kB/s 
Collecting gensim (from -r requirements.txt (line 4))
  Using cached gensim-0.12.1.tar.gz
Collecting docx (from -r requirements.txt (line 5))
  Using cached docx-0.2.4.tar.gz
Collecting pyth (from -r requirements.txt (line 6))
  Using cached pyth-0.6.0.tar.gz
Collecting pymongo (from -r requirements.txt (line 7))
/Users/aljohnson/code/rosetta/rosetta_env/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
  Downloading pymongo-3.0.3-cp27-none-macosx_10_8_intel.whl (239kB)
    100% |████████████████████████████████| 241kB 2.0MB/s 
Collecting MySQL-python (from -r requirements.txt (line 8))
  Using cached MySQL-python-1.2.5.zip
    Complete output from command python setup.py egg_info:
    sh: mysql_config: command not found
    Traceback (most recent call last):
      File "<string>", line 20, in <module>
      File "/private/var/folders/vj/_mcyrpkn30d2tph7c56yvzxxf5_jlv/T/pip-build-ylIxmf/MySQL-python/setup.py", line 17, in <module>
        metadata, options = get_config()
      File "setup_posix.py", line 43, in get_config
        libs = mysql_config("libs_r")
      File "setup_posix.py", line 25, in mysql_config
        raise EnvironmentError("%s not found" % (mysql_config.path,))
    EnvironmentError: mysql_config not found

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/vj/_mcyrpkn30d2tph7c56yvzxxf5_jlv/T/pip-build-ylIxmf/MySQL-python
(rosetta_env)

At this point I'm not sure what the hell is going on. Its probably my fault in the end but, essentially, this is seeming a lot harder than it should be. Just to import rosetta.

When the token_col dictionary is updated it would be good to also update an overall count for each token, to later use for feature selection/filtering etc.

Perhaps the self.token_col_map should be self.token_col_count_map or there should be two separate attributes self.token_col_map and self.token_count_map - thoughts?