Update requirements

Generated with poetry export:

    $ poetry export --without-hashes -f requirements.txt > requirements.txt
    $ poetry export --without-hashes --dev -f requirements.txt > requirements-dev.txt

I am trying `--without-hashes` to work around an error on pip install
when running in CI:

    ERROR: In --require-hashes mode, all requirements must have their versions pinned with ==.

CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+### Added
+- Ability to check for, and fix, "mojibake" characters using [ftfy](https://github.com/LuminosoInsight/python-ftfy)
+
+### Updated
+- Python dependencies
+
 ## [0.4.7] - 2021-03-17
 ### Changed
 - Fixing invalid multi-value separators like `|` and `|||` is no longer class-

README.md

@@ -20,7 +20,9 @@ If you use the DSpace CSV metadata quality checker please cite:
 - Perform [Unicode normalization](https://withblue.ink/2019/03/11/why-you-need-to-normalize-unicode-strings.html) on strings using `--unsafe-fixes`
 - Remove unnecessary Unicode like [non-breaking spaces](https://en.wikipedia.org/wiki/Non-breaking_space), [replacement characters](https://en.wikipedia.org/wiki/Specials_(Unicode_block)#Replacement_character), etc
 - Check for "suspicious" characters that indicate encoding or copy/paste issues, for example "foreˆt" should be "forêt"
+- Check for "mojibake" characters (and attempt to fix with `--unsafe-fixes`)
 - Remove duplicate metadata values
+- Check for duplicate items, using the title, type, and date issued as an indicator
 
 ## Installation
 The easiest way to install CSV Metadata Quality is with [poetry](https://python-poetry.org):
@@ -61,7 +63,7 @@ While it is *theoretically* possible for a single `|` character to be used legit
 This will also remove unnecessary trailing multi-value separators, for example `Kenya||Tanzania||`.
 
 ## Unsafe Fixes
-You can enable several "unsafe" fixes with the `--unsafe-fixes` option. Currently this will remove newlines and perform Unicode normalization.
+You can enable several "unsafe" fixes with the `--unsafe-fixes` option. Currently this will remove newlines, perform Unicode normalization, and attempt to fix "mojibake" characters.
 
 ### Newlines
 This is considered "unsafe" because some systems give special importance to vertical space and render it properly. DSpace does not support rendering newlines in its XMLUI and has, at times, suffered from parsing errors that cause the import process to fail if an input file had newlines. The `--unsafe-fixes` option strips Unix line feeds (U+000A).
@@ -74,6 +76,14 @@ This is considered "unsafe" because some systems give special importance to vert
 
 Read more about [Unicode normalization](https://withblue.ink/2019/03/11/why-you-need-to-normalize-unicode-strings.html).
 
+### Encoding Issues aka "Mojibake"
+[Mojibake](https://en.wikipedia.org/wiki/Mojibake) is a phenomenon that occurs when text is decoded using an unintended character encoding. This usually presents itself in the form of strange, garbled characters in the text. Enabling "unsafe" fixes will attempt to correct these, for example:
+
+- CIAT Publicaçao → CIAT Publicaçao
+- CIAT Publicación → CIAT Publicación
+
+Pay special attention to the output of the script as well as the resulting file to make sure no new issues have been introduced. The ideal way to solve these issues is to avoid it in the first place. See [this guide about opening CSVs in UTF-8 format in Excel](https://www.itg.ias.edu/content/how-import-csv-file-uses-utf-8-character-encoding-0).
+
 ## AGROVOC Validation
 You can enable validation of metadata values in certain fields against the AGROVOC REST API with the `--agrovoc-fields` option. For example, in addition to agricultural subjects, many countries and regions are also present AGROVOC. Enable this validation by specifying a comma-separated list of fields:
 
@@ -116,10 +126,6 @@ This currently uses the [Python langid](https://github.com/saffsd/langid.py) lib
   - Warn if item is Open Access, but missing a license
   - Warn if item has an ISSN but no journal title
   - Update journal titles from ISSN
-- Check for duplicates
-  - If I check titles only, then I might miss if one is a Report and another is a Presentation
-  - I could just check each item against each other item, but that sounds slow...
-  - Perhaps I could check for the number of unique values in a few rows, like title and doi, and see if it is the same as the total number of items
 
 ## License
 This work is licensed under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html).

csv_metadata_quality/__main__.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
 from sys import argv
 
 from csv_metadata_quality import app

csv_metadata_quality/app.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
 import argparse
 import re
 import signal
@@ -107,6 +109,13 @@ def run(argv):
         # Check: suspicious characters
         df[column].apply(check.suspicious_characters, field_name=column)
 
+        # Check: mojibake
+        df[column].apply(check.mojibake, field_name=column)
+
+        # Fix: mojibake
+        if args.unsafe_fixes:
+            df[column] = df[column].apply(fix.mojibake, field_name=column)
+
         # Fix: invalid and unnecessary multi-value separators
         df[column] = df[column].apply(fix.separators, field_name=column)
         # Run whitespace fix again after fixing invalid separators
@@ -155,13 +164,16 @@ def run(argv):
 
     # Check: duplicate items
     # We extract just the title, type, and date issued columns to analyze
-    duplicates_df = df.filter(
-        regex=r"dcterms\.title|dc\.title|dcterms\.type|dc\.type|dcterms\.issued|dc\.date\.issued"
-    )
-    check.duplicate_items(duplicates_df)
+    try:
+        duplicates_df = df.filter(
+            regex=r"dcterms\.title|dc\.title|dcterms\.type|dc\.type|dcterms\.issued|dc\.date\.issued"
+        )
+        check.duplicate_items(duplicates_df)
 
-    # Delete the temporary duplicates DataFrame
-    del duplicates_df
+        # Delete the temporary duplicates DataFrame
+        del duplicates_df
+    except IndexError:
+        pass
 
     ##
     # Perform some checks on rows so we can consider items as a whole rather

csv_metadata_quality/check.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
 import os
 import re
 from datetime import datetime, timedelta
@@ -11,6 +13,8 @@ from pycountry import languages
 from stdnum import isbn as stdnum_isbn
 from stdnum import issn as stdnum_issn
 
+from csv_metadata_quality.util import is_mojibake
+
 
 def issn(field):
     """Check if an ISSN is valid.
@@ -174,13 +178,9 @@ def language(field):
         if len(value) == 2:
             if not languages.get(alpha_2=value):
                 print(f"{Fore.RED}Invalid ISO 639-1 language: {Fore.RESET}{value}")
-
-                pass
         elif len(value) == 3:
             if not languages.get(alpha_3=value):
                 print(f"{Fore.RED}Invalid ISO 639-3 language: {Fore.RESET}{value}")
-
-                pass
         else:
             print(f"{Fore.RED}Invalid language: {Fore.RESET}{value}")
 
@@ -301,8 +301,6 @@ def spdx_license_identifier(field):
         if value not in spdx_license_list.LICENSES:
             print(f"{Fore.YELLOW}Non-SPDX license identifier: {Fore.RESET}{value}")
 
-            pass
-
     return
 
 
@@ -345,3 +343,22 @@ def duplicate_items(df):
                 )
             else:
                 items.append(item_title_type_date)
+
+
+def mojibake(field, field_name):
+    """Check for mojibake (text that was encoded in one encoding and decoded in
+    in another, perhaps multiple times). See util.py.
+
+    Prints the string if it contains suspected mojibake.
+    """
+
+    # Skip fields with missing values
+    if pd.isna(field):
+        return
+
+    if is_mojibake(field):
+        print(
+            f"{Fore.YELLOW}Possible encoding issue ({field_name}): {Fore.RESET}{field}"
+        )
+
+    return

csv_metadata_quality/experimental.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
 import re
 
 import langid

csv_metadata_quality/fix.py

@@ -1,10 +1,13 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
 import re
 from unicodedata import normalize
 
 import pandas as pd
 from colorama import Fore
+from ftfy import fix_text
 
-from csv_metadata_quality.util import is_nfc
+from csv_metadata_quality.util import is_mojibake, is_nfc
 
 
 def whitespace(field, field_name):
@@ -253,3 +256,22 @@ def normalize_unicode(field, field_name):
         field = normalize("NFC", field)
 
     return field
+
+
+def mojibake(field, field_name):
+    """Attempts to fix mojibake (text that was encoded in one encoding and deco-
+    ded in another, perhaps multiple times). See util.py.
+
+    Return fixed string.
+    """
+
+    # Skip fields with missing values
+    if pd.isna(field):
+        return field
+
+    if is_mojibake(field):
+        print(f"{Fore.GREEN}Fixing encoding issue ({field_name}): {Fore.RESET}{field}")
+
+        return fix_text(field)
+    else:
+        return field

csv_metadata_quality/util.py

@@ -1,3 +1,8 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
+from ftfy.badness import sequence_weirdness
+
+
 def is_nfc(field):
     """Utility function to check whether a string is using normalized Unicode.
     Python's built-in unicodedata library has the is_normalized() function, but
@@ -12,3 +17,35 @@ def is_nfc(field):
     from unicodedata import normalize
 
     return field == normalize("NFC", field)
+
+
+def is_mojibake(field):
+    """Determines whether a string contains mojibake.
+
+    We commonly deal with CSV files that were *encoded* in UTF-8, but decoded
+    as something else like CP-1252 (Windows Latin). This manifests in the form
+    of "mojibake", for example:
+
+        - CIAT Publicaçao
+        - CIAT Publicación
+
+    This uses the excellent "fixes text for you" (ftfy) library to determine
+    whether a string contains characters that have been encoded in one encoding
+    and decoded in another.
+
+    Inspired by this code snippet from Martijn Pieters on StackOverflow:
+    https://stackoverflow.com/questions/29071995/identify-garbage-unicode-string-using-python
+
+    Return boolean.
+    """
+    if not sequence_weirdness(field):
+        # Nothing weird, should be okay
+        return False
+    try:
+        field.encode("sloppy-windows-1252")
+    except UnicodeEncodeError:
+        # Not CP-1252 encodable, probably fine
+        return False
+    else:
+        # Encodable as CP-1252, Mojibake alert level high
+        return True

csv_metadata_quality/version.py

@@ -1 +1,3 @@
-VERSION = "0.4.7"
+# SPDX-License-Identifier: GPL-3.0-only
+
+VERSION = "0.4.8-dev"

data/test.csv

@@ -32,3 +32,4 @@ Unnecessary multi-value separator,2021-01-03,0378-5955||,,,,,,,
 Invalid SPDX license identifier,2021-03-11,,,,,,,CC-BY,
 Duplicate Title,2021-03-17,,,,,,,,Report
 Duplicate Title,2021-03-17,,,,,,,,Report
+Mojibake,2021-03-18,,,,CIAT Publicaçao,,,,Report

poetry.lock

@@ -83,21 +83,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "20.3.0"
+version = "21.2.0"
 description = "Classes Without Boilerplate"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
-docs = ["furo", "sphinx", "zope.interface"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
 
 [[package]]
 name = "babel"
-version = "2.9.0"
+version = "2.9.1"
 description = "Internationalization utilities"
 category = "dev"
 optional = false
@@ -138,7 +138,7 @@ d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
 
 [[package]]
 name = "certifi"
-version = "2020.12.5"
+version = "2021.5.30"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
@@ -154,11 +154,15 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "click"
-version = "7.1.2"
+version = "8.0.1"
 description = "Composable command line interface toolkit"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [[package]]
 name = "colorama"
@@ -193,23 +197,23 @@ python-versions = "*"
 
 [[package]]
 name = "decorator"
-version = "4.4.2"
+version = "5.0.9"
 description = "Decorators for Humans"
 category = "dev"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*"
+python-versions = ">=3.5"
 
 [[package]]
 name = "et-xmlfile"
-version = "1.0.1"
+version = "1.1.0"
 description = "An implementation of lxml.xmlfile for the standard library"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "flake8"
-version = "3.9.0"
+version = "3.9.2"
 description = "the modular source code checker: pep8 pyflakes and co"
 category = "dev"
 optional = false
@@ -221,9 +225,20 @@ mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
 
+[[package]]
+name = "ftfy"
+version = "5.9"
+description = "Fixes some problems with Unicode text after the fact"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+wcwidth = "*"
+
 [[package]]
 name = "greenlet"
-version = "1.0.0"
+version = "1.1.0"
 description = "Lightweight in-process concurrent programming"
 category = "dev"
 optional = false
@@ -242,7 +257,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "3.7.3"
+version = "4.5.0"
 description = "Read metadata from Python packages"
 category = "dev"
 optional = false
@@ -254,7 +269,7 @@ zipp = ">=0.5"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "iniconfig"
@@ -266,7 +281,7 @@ python-versions = "*"
 
 [[package]]
 name = "ipython"
-version = "7.21.0"
+version = "7.24.1"
 description = "IPython: Productive Interactive Computing"
 category = "dev"
 optional = false
@@ -278,6 +293,7 @@ backcall = "*"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
 jedi = ">=0.16"
+matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
 prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
@@ -285,7 +301,7 @@ pygments = "*"
 traitlets = ">=4.2"
 
 [package.extras]
-all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.14)", "pygments", "qtconsole", "requests", "testpath"]
+all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.17)", "pygments", "qtconsole", "requests", "testpath"]
 doc = ["Sphinx (>=1.3)"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
@@ -293,7 +309,7 @@ nbformat = ["nbformat"]
 notebook = ["notebook", "ipywidgets"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.14)"]
+test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"]
 
 [[package]]
 name = "ipython-genutils"
@@ -316,7 +332,7 @@ six = "*"
 
 [[package]]
 name = "isort"
-version = "5.7.0"
+version = "5.8.0"
 description = "A Python utility / library to sort Python imports."
 category = "dev"
 optional = false
@@ -364,6 +380,17 @@ python-versions = "*"
 [package.dependencies]
 six = ">=1.6.1"
 
+[[package]]
+name = "matplotlib-inline"
+version = "0.1.2"
+description = "Inline Matplotlib backend for Jupyter"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+traitlets = "*"
+
 [[package]]
 name = "mccabe"
 version = "0.6.1"
@@ -382,7 +409,7 @@ python-versions = "*"
 
 [[package]]
 name = "numpy"
-version = "1.20.1"
+version = "1.20.3"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -412,7 +439,7 @@ pyparsing = ">=2.0.2"
 
 [[package]]
 name = "pandas"
-version = "1.2.3"
+version = "1.2.4"
 description = "Powerful data structures for data analysis, time series, and statistics"
 category = "main"
 optional = false
@@ -436,7 +463,7 @@ python-versions = "*"
 
 [[package]]
 name = "parso"
-version = "0.8.1"
+version = "0.8.2"
 description = "A Python Parser"
 category = "dev"
 optional = false
@@ -489,7 +516,7 @@ dev = ["pre-commit", "tox"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.17"
+version = "3.0.18"
 description = "Library for building powerful interactive command lines in Python"
 category = "dev"
 optional = false
@@ -532,7 +559,7 @@ python-versions = "*"
 
 [[package]]
 name = "pyflakes"
-version = "2.3.0"
+version = "2.3.1"
 description = "passive checker of Python programs"
 category = "dev"
 optional = false
@@ -540,7 +567,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.8.1"
+version = "2.9.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
@@ -548,7 +575,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "pyicu"
-version = "2.6"
+version = "2.7.3"
 description = "Python extension wrapping the ICU C++ API"
 category = "dev"
 optional = false
@@ -564,7 +591,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "pytest"
-version = "6.2.2"
+version = "6.2.4"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
@@ -609,11 +636,11 @@ six = ">=1.5"
 
 [[package]]
 name = "python-slugify"
-version = "4.0.1"
+version = "5.0.2"
 description = "A Python Slugify application that handles Unicode"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
 
 [package.dependencies]
 text-unidecode = ">=1.3"
@@ -652,7 +679,7 @@ python-versions = "*"
 
 [[package]]
 name = "regex"
-version = "2020.11.13"
+version = "2021.4.4"
 description = "Alternative regular expression module, to replace re."
 category = "dev"
 optional = false
@@ -689,7 +716,7 @@ requests = ">=1.1.0"
 
 [[package]]
 name = "six"
-version = "1.15.0"
+version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
 category = "main"
 optional = false
@@ -705,7 +732,7 @@ python-versions = "*"
 
 [[package]]
 name = "sqlalchemy"
-version = "1.4.0"
+version = "1.4.18"
 description = "Database Abstraction Library"
 category = "dev"
 optional = false
@@ -717,6 +744,7 @@ importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
+aiosqlite = ["greenlet (!=0.4.17)", "aiosqlite"]
 asyncio = ["greenlet (!=0.4.17)"]
 mariadb_connector = ["mariadb (>=1.0.1)"]
 mssql = ["pyodbc"]
@@ -732,6 +760,7 @@ postgresql_pg8000 = ["pg8000 (>=1.16.6)"]
 postgresql_psycopg2binary = ["psycopg2-binary"]
 postgresql_psycopg2cffi = ["psycopg2cffi"]
 pymysql = ["pymysql (<1)", "pymysql"]
+sqlcipher = ["sqlcipher3-binary"]
 
 [[package]]
 name = "termcolor"
@@ -773,7 +802,7 @@ test = ["pytest"]
 
 [[package]]
 name = "typed-ast"
-version = "1.4.2"
+version = "1.4.3"
 description = "a fork of Python 2 and 3 ast modules with type comment support"
 category = "dev"
 optional = false
@@ -781,7 +810,7 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "3.7.4.3"
+version = "3.10.0.0"
 description = "Backported and Experimental Type Hints for Python 3.5+"
 category = "dev"
 optional = false
@@ -789,22 +818,22 @@ python-versions = "*"
 
 [[package]]
 name = "urllib3"
-version = "1.26.4"
+version = "1.26.5"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
 
 [package.extras]
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 name = "wcwidth"
 version = "0.2.5"
 description = "Measures the displayed width of unicode strings in a terminal"
-category = "dev"
+category = "main"
 optional = false
 python-versions = "*"
 
@@ -831,7 +860,7 @@ testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pyt
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-    {file = "typing_extensions-3.7.4.3.tar.gz", hash = "sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c"},
+    {file = "typing_extensions-3.10.0.0-py2-none-any.whl", hash = "sha256:0ac0f89795dd19de6b97debb0c6af1c70987fd80a2d62d1958f7e56fcc31b497"},
+    {file = "typing_extensions-3.10.0.0-py3-none-any.whl", hash = "sha256:779383f6086d90c99ae41cf0ff39aac8a7937a9283ce0a414e5dd782f4c94a84"},
+    {file = "typing_extensions-3.10.0.0.tar.gz", hash = "sha256:50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342"},
 ]
 urllib3 = [
-    {file = "urllib3-1.26.4-py2.py3-none-any.whl", hash = "sha256:2f4da4594db7e1e110a944bb1b551fdf4e6c136ad42e4234131391e21eb5b0df"},
-    {file = "urllib3-1.26.4.tar.gz", hash = "sha256:e7b021f7241115872f92f43c6508082facffbd1c048e3c6e2bb9c2a157e28937"},
+    {file = "urllib3-1.26.5-py2.py3-none-any.whl", hash = "sha256:753a0374df26658f99d826cfe40394a686d05985786d946fbe4165b5148f5a7c"},
+    {file = "urllib3-1.26.5.tar.gz", hash = "sha256:a7acd0977125325f516bda9735fa7142b909a8d01e8b2e4c8108d0984e6e0098"},
 ]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "csv-metadata-quality"
-version = "0.4.7"
+version = "0.4.8-dev"
 description="A simple, but opinionated CSV quality checking and fixing pipeline for CSVs in the DSpace ecosystem."
 authors = ["Alan Orth <alan.orth@gmail.com>"]
 license="GPL-3.0-only"
@@ -21,6 +21,7 @@ pycountry = "^19.8.18"
 langid = "^1.1.6"
 colorama = "^0.4.4"
 spdx-license-list = "^0.5.2"
+ftfy = "^5.9"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.1.1"

requirements-dev.txt

@@ -5,71 +5,73 @@ agate==1.6.2
 appdirs==1.4.4; python_version >= "3.6"
 appnope==0.1.2; python_version >= "3.7" and python_version < "4.0" and sys_platform == "darwin"
 atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
-attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
-babel==2.9.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+attrs==21.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+babel==2.9.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 backcall==0.2.0; python_version >= "3.7" and python_version < "4.0"
 black==20.8b1; python_version >= "3.6"
-certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+certifi==2021.5.30; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
-click==7.1.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+click==8.0.1; python_version >= "3.6"
 colorama==0.4.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 csvkit==1.0.5
 dbfread==2.0.7
-decorator==4.4.2; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.2.0"
-et-xmlfile==1.0.1; python_version >= "3.6"
-flake8==3.9.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
-greenlet==1.0.0; python_version >= "3" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3"
+decorator==5.0.9; python_version >= "3.7" and python_version < "4.0"
+et-xmlfile==1.1.0; python_version >= "3.6"
+flake8==3.9.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+ftfy==5.9; python_version >= "3.5"
+greenlet==1.1.0; python_version >= "3" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3"
 idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
-importlib-metadata==3.7.3; python_version < "3.8" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.5.0" and python_version < "3.8" and python_version >= "3.6") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.6")
+importlib-metadata==4.5.0; python_version < "3.8" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.5.0" and python_version < "3.8" and python_version >= "3.6") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.6")
 iniconfig==1.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 ipython-genutils==0.2.0; python_version >= "3.7" and python_version < "4.0"
-ipython==7.21.0; python_version >= "3.7" and python_version < "4.0"
+ipython==7.24.1; python_version >= "3.7" and python_version < "4.0"
 isodate==0.6.0
-isort==5.7.0; python_version >= "3.6" and python_version < "4.0"
+isort==5.8.0; python_version >= "3.6" and python_version < "4.0"
 jedi==0.18.0; python_version >= "3.7" and python_version < "4.0"
 langid==1.1.6
 leather==0.3.3
+matplotlib-inline==0.1.2; python_version >= "3.7" and python_version < "4.0"
 mccabe==0.6.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 mypy-extensions==0.4.3; python_version >= "3.6"
-numpy==1.20.1; python_version >= "3.7" and python_full_version >= "3.7.1"
+numpy==1.20.3; python_version >= "3.7" and python_full_version >= "3.7.1"
 openpyxl==3.0.7; python_version >= "3.6"
 packaging==20.9; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
-pandas==1.2.3; python_full_version >= "3.7.1"
+pandas==1.2.4; python_full_version >= "3.7.1"
 parsedatetime==2.6
-parso==0.8.1; python_version >= "3.7" and python_version < "4.0"
+parso==0.8.2; python_version >= "3.7" and python_version < "4.0"
 pathspec==0.8.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
 pexpect==4.8.0; python_version >= "3.7" and python_version < "4.0" and sys_platform != "win32"
 pickleshare==0.7.5; python_version >= "3.7" and python_version < "4.0"
 pluggy==0.13.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
-prompt-toolkit==3.0.17; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.1"
+prompt-toolkit==3.0.18; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.1"
 ptyprocess==0.7.0; python_version >= "3.7" and python_version < "4.0" and sys_platform != "win32"
 py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 pycodestyle==2.7.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 pycountry==19.8.18
-pyflakes==2.3.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
-pygments==2.8.1; python_version >= "3.7" and python_version < "4.0"
-pyicu==2.6
+pyflakes==2.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+pygments==2.9.0; python_version >= "3.7" and python_version < "4.0"
+pyicu==2.7.3
 pyparsing==2.4.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 pytest-clarity==0.3.0a0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
-pytest==6.2.2; python_version >= "3.6"
+pytest==6.2.4; python_version >= "3.6"
 python-dateutil==2.8.1; python_full_version >= "3.7.1"
-python-slugify==4.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+python-slugify==5.0.2; python_version >= "3.6"
 python-stdnum==1.16
 pytimeparse==1.1.8
 pytz==2021.1; python_full_version >= "3.7.1"
-regex==2020.11.13; python_version >= "3.6"
+regex==2021.4.4; python_version >= "3.6"
 requests-cache==0.5.2
 requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
-six==1.15.0; python_full_version >= "3.7.1"
+six==1.16.0; python_full_version >= "3.7.1"
 spdx-license-list==0.5.2
-sqlalchemy==1.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+sqlalchemy==1.4.18; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
 termcolor==1.1.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
-text-unidecode==1.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+text-unidecode==1.3; python_version >= "3.6"
 toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 traitlets==5.0.5; python_version >= "3.7" and python_version < "4.0"
-typed-ast==1.4.2; python_version >= "3.6"
-typing-extensions==3.7.4.3; python_version < "3.8" and python_version >= "3.6"
-urllib3==1.26.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+typed-ast==1.4.3; python_version >= "3.6"
+typing-extensions==3.10.0.0; python_version < "3.8" and python_version >= "3.6"
+urllib3==1.26.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
 wcwidth==0.2.5; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.1"
 xlrd==1.2.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
 zipp==3.4.1; python_version < "3.8" and python_version >= "3.6"

requirements.txt

@@ -1,17 +1,19 @@
-certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+certifi==2021.5.30; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 colorama==0.4.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+ftfy==5.9; python_version >= "3.5"
 idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 langid==1.1.6
-numpy==1.20.1; python_version >= "3.7" and python_full_version >= "3.7.1"
-pandas==1.2.3; python_full_version >= "3.7.1"
+numpy==1.20.3; python_version >= "3.7" and python_full_version >= "3.7.1"
+pandas==1.2.4; python_full_version >= "3.7.1"
 pycountry==19.8.18
 python-dateutil==2.8.1; python_full_version >= "3.7.1"
 python-stdnum==1.16
 pytz==2021.1; python_full_version >= "3.7.1"
 requests-cache==0.5.2
 requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
-six==1.15.0; python_full_version >= "3.7.1"
+six==1.16.0; python_full_version >= "3.7.1"
 spdx-license-list==0.5.2
-urllib3==1.26.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+urllib3==1.26.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+wcwidth==0.2.5; python_version >= "3.5"
 xlrd==1.2.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")

setup.py

@@ -14,7 +14,7 @@ install_requires = [
 
 setuptools.setup(
     name="csv-metadata-quality",
-    version="0.4.7",
+    version="0.4.8-dev",
     author="Alan Orth",
     author_email="aorth@mjanja.ch",
     description="A simple, but opinionated CSV quality checking and fixing pipeline for CSVs in the DSpace ecosystem.",

tests/test_check.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
 import pandas as pd
 from colorama import Fore
 
@@ -339,3 +341,29 @@ def test_check_duplicate_item(capsys):
         captured.out
         == f"{Fore.YELLOW}Possible duplicate (dc.title): {Fore.RESET}{item_title}\n"
     )
+
+
+def test_check_no_mojibake():
+    """Test string with no mojibake."""
+
+    field = "CIAT Publicaçao"
+    field_name = "dcterms.isPartOf"
+
+    result = check.mojibake(field, field_name)
+
+    assert result == None
+
+
+def test_check_mojibake(capsys):
+    """Test string with mojibake."""
+
+    field = "CIAT Publicaçao"
+    field_name = "dcterms.isPartOf"
+
+    result = check.mojibake(field, field_name)
+
+    captured = capsys.readouterr()
+    assert (
+        captured.out
+        == f"{Fore.YELLOW}Possible encoding issue ({field_name}): {Fore.RESET}{field}\n"
+    )

tests/test_fix.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: GPL-3.0-only
+
 import csv_metadata_quality.fix as fix
 
 
@@ -108,3 +110,12 @@ def test_fix_decomposed_unicode():
     field_name = "dc.contributor.author"
 
     assert fix.normalize_unicode(value, field_name) == "Ouédraogo, Mathieu"
+
+
+def test_fix_mojibake():
+    """Test string with no mojibake."""
+
+    field = "CIAT Publicaçao"
+    field_name = "dcterms.isPartOf"
+
+    assert fix.mojibake(field, field_name) == "CIAT Publicaçao"