anonymoUUs 0.0.8
A tool to substitue patterns/names in a file tree
License: MIT
Requires Python: >=3.6

# anonymoUUs

This description can be found [on GitHub here](https://github.com/UtrechtUniversity/anonymouus)

anonymoUUs facilitates the replacement of keywords or regex-patterns within a file tree or zipped archive. It recursively traverses the tree, opens supported files and substitutes any found pattern or keyword with a replacement. Besides contents, anonymoUUs will substitue keywords/patterns in file/folder-paths as well.

The result will be either a copied or replaced version of the original file-tree with all substitutions made.

As of now, anonymoUUs supports text-based files, like .txt, .html, .json and .csv. UTF-8 encoding is assumed. Besides text files, anonymoUUs is also able to handle (nested) zip archives. These archives will be unpacked in a temp folder, processed and zipped again.

## Installation

`$ pip install anonymoUUs`

## Usage

In order to replace words or patterns you need a replacement-mapping in the form of:
1. a dictionary - the keys will be replaced by the values
2. the path to a csv file - a csv file will be converted in a dictionary, the first column provides keys, the second value provides values. Path can be a String, Path or PosixPath!
3. a function - a replacement function can be passed if a pattern is used. The function takes a found match and should return its replacement. The function must have at least one input argument.

### Example of replacement with a dictionary

Import the Anomymize class in your code and create an anonymization object like this:

```python
from anonymoUUs import Anonymize

# refer to csv files in which keywords and substitutions are paired
anonymize_csv = Anonymize('/Users/casper/Desktop/keys.csv')

# using a dictionary instead of a csv file:
my_dict = {
    'A1234': 'aaaa',
    'B9876': 'bbbb',
}
anonymize_dict = Anonymize(my_dict)
```

Putting regular expression in dictionaries is also possible.When using a dictionary only (absence of the `pattern` argument), the keys-pattern will be replaced by its value:

```
anon = Anonymize(
    {
        'regular-key': 'replacement-1',
        re.compile('ca.*?er'): 'replacement-2'
    }
)
```

### Example of replacement with a CSV file

```python
# specifying a zip-format to zip unpacked archives after processing (.zip is default)
anonymize_zip = Anonymize('/Users/casper/Desktop/keys.csv')
```

When using a csv-file, anonymoUUs will assume your file contains two columns: the left column contains the keywords which need to be replaced, the right column contains their substitutions. **Column headers are mandatory**, but don't have to follow a specific format.

It is possible to add a regular expression as keyword in the csv-file. Make sure they start with the prefix 'r#'. Example:

```
r#ca.*?er, replacement_string
```

The key will be compiles as a regex and replace every match with 'replacement_string'.


### Example of replacement by regex pattern and function

If you are replacing with a pattern you can also use a function to 'calculate' the replacement string:

```python
def replace(match, **kwargs):
    result = 'default-replacement'
    match = int(match)
    threshold = kwargs.get("threshold", 4000)
    if match < threshold:
        result = 'special-replacement'
    return result

anon = Anonymize(replace, pattern=r'\d{4}', threshold=1000)
anon.substitute(
    '/Users/casperkaandorp/Desktop/test.json', 
    '/Users/casperkaandorp/Desktop/result-folder'
)
```
Note the possibility to provide additional arguments when you initialize an Anonymize object that will be passed to the replcement function (in the previous example, the `threshold` is passed to the `replace` function).

### Other arguments

Performance is probably best when your keywords can be generalized into a single regular expressions. anonymoUUs will search these patterns and replace them instead of matching the entire dictionary/csv-file against file contents or file/folder-paths. Example:

```
anonymize_regex = Anonymize(my_dict, pattern=r'[A-B]\d{4}')
```

By default is case sensitive by default. The regular expressions that take care of the replacements can be modified by using the `flag` parameter. It takes one or more variables [which can be found here](https://docs.python.org/3/library/re.html). Multiple variables are combined by a bitwise OR (the | operator). Example for a case-insensitive substitution:

```
anonymize_regex = Anonymize(my_dict, flags=re.IGNORECASE)
```

By using the `use_word_boundaries` argument (defaults to False), the algorithm ignores substring matches. If 'ted' is a key in your dictionary, without `use_word_boundaries` the algorithm will replace the 'ted' part in f.i. 'created_at'. You can overcome this problem by setting `use_word_boundaries` to True. It will put the `\b`-anchor around your regex pattern or dictionary keys. The beauty of the boundary anchors is that '@' is considered a boundary as well, and thus names in email addresses can be replaced. Example:

```
anonymize_regex = Anonymize(my_dict, use_word_boundaries=True)
```

It is also to specify how to re-zip unzipped folders:

```python
# specifying a zip-format to zip unpacked archives after processing (.zip is default)
anonymize_zip = Anonymize('/Users/casper/Desktop/keys.csv', zip_format='gztar')
```

### Windows usage

There is an issue with creating zip archives. Make sure you **run anonymoUUs as administrator**.

### Inplace replacements vs. replacements in a copy

anonymoUUs is able to create a copy of the processed file-tree or replace it. The `substitute` method takes a mandatory source-path argument (path to a file, folder or zip-archive, either a string or a [Path](https://docs.python.org/3/library/pathlib.html#basic-use) object) and an optional target-path argument (again, a string or [Path](https://docs.python.org/3/library/pathlib.html#basic-use) object). The target **needs to refer to a folder**, which can't be a sub-folder of the source-folder. The target-folder will be created if it doesn't exist.

When the target argument is provided, anonymoUUs will create a processed copy of the source into the target-folder. If the source is a single file, and the file path does not contain elements that will be replaced, and the target-folder is identical to the source folder, than the processed result will get a 'copy' extension to prevent overwriting.

When the target argument is omitted, the source will be overwritten by a processed version of it:

```
# process the datadownload.zip file, replace all patterns and write
# a copy to the 'bucket' folder.
anonymize_regex.substitute(
    '/Users/casper/Desktop/datadownload.zip', 
    '/Users/casper/Desktop/bucket'
)

# process the 'download' folder and replace the original by its processed 
# version
anonymize_regex.substitute('/Users/casper/Desktop/download')

# process a single file, and replace it
anonymize_regex.substitute('/Users/casper/Desktop/my_file.json')
```

### Reading contents of a file

Files will be opened depending on their extension. Non refognized extensions will be skipped. The standard version of this package assumes 'UTF-8' encoding. Errors are going to be ignored. Since reading file-contents is done with a single function, it will be easy to adjust (different encodings,etc) by overloading it in an extension:

```python
# standard reading function
def _read_file(self, source: Path):
    f = open(source, 'r', encoding='utf-8', errors='ignore')
    contents = list(f)
    f.close()
    return contents
```

## Todo

Cleaning up this document

Testing! Sweet momma, it needs testing.