CHANGELOG.md

@@ -7,7 +7,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## Unreleased
 ### Added
 - Ability to check for, and fix, "mojibake" characters using [ftfy](https://github.com/LuminosoInsight/python-ftfy)
-- Ability to check if the item's title exists in the citation
 
 ### Updated
 - Python dependencies

csv_metadata_quality/app.py

@@ -109,11 +109,12 @@ def run(argv):
         # Check: suspicious characters
         df[column].apply(check.suspicious_characters, field_name=column)
 
-        # Fix: mojibake. If unsafe fixes are not enabled then we only check.
+        # 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)
-        else:
-            df[column].apply(check.mojibake, field_name=column)
 
         # Fix: invalid and unnecessary multi-value separators
         df[column] = df[column].apply(fix.separators, field_name=column)
@@ -194,9 +195,6 @@ def run(argv):
         # Check: citation DOI
         check.citation_doi(df_transposed[column])
 
-        # Check: title in citation
-        check.title_in_citation(df_transposed[column])
-
         if args.experimental_checks:
             experimental.correct_language(df_transposed[column])
 

csv_metadata_quality/check.py

@@ -410,40 +410,3 @@ def citation_doi(row):
             )
 
     return
-
-
-def title_in_citation(row):
-    """Check for the scenario where an item's title is missing from its cita-
-    tion. This could mean that it is missing entirely, or perhaps just exists
-    in a different format (whitespace, accents, etc).
-
-    Function prints a warning if the title does not appear in the citation.
-    """
-    # Initialize some variables at global scope so that we can set them in the
-    # loop scope below and still be able to access them afterwards.
-    title = ""
-    citation = ""
-
-    # Iterate over the labels of the current row's values to get the names of
-    # the title and citation columns. Then we check if the title is present in
-    # the citation.
-    for label in row.axes[0]:
-        # Skip fields with missing values
-        if pd.isna(row[label]):
-            continue
-
-        # Find the name of the title column
-        match = re.match(r"^(dc|dcterms)\.title.*$", label)
-        if match is not None:
-            title = row[label]
-
-        # Find the name of the citation column
-        match = re.match(r"^.*?[cC]itation.*$", label)
-        if match is not None:
-            citation = row[label]
-
-    if citation != "":
-        if title not in citation:
-            print(f"{Fore.YELLOW}Title is not present in citation: {Fore.RESET}{title}")
-
-    return

data/test.csv

@@ -33,5 +33,4 @@ 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,,,,Publicaçao CIAT,,,,Report,,
-"DOI in citation, but missing cg.identifier.doi",2021-10-06,,,,,,,,,"Orth, A. 2021. DOI in citation, but missing cg.identifier.doi. doi: 10.1186/1743-422X-9-218",
+"DOI in citation, but missing cg.identifier.doi",2021-10-06,,,,,,,,,"Orth, A. 2021. Testing all the things. doi: 10.1186/1743-422X-9-218",
-Title missing from citation,2021-12-05,,,,,,,,,"Orth, A. 2021. Title missing f rom citation.",

poetry.lock

@@ -153,7 +153,7 @@ python-versions = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "2.0.9"
+version = "2.0.8"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
@@ -315,7 +315,7 @@ python-versions = "*"
 
 [[package]]
 name = "ipython"
-version = "7.30.1"
+version = "7.30.0"
 description = "IPython: Productive Interactive Computing"
 category = "dev"
 optional = false
@@ -514,7 +514,7 @@ future = "*"
 
 [[package]]
 name = "parso"
-version = "0.8.3"
+version = "0.8.2"
 description = "A Python Parser"
 category = "dev"
 optional = false
@@ -793,7 +793,7 @@ test = ["black (==20.8b1)", "flake8", "flake8-comprehensions", "flake8-polyfill"
 
 [[package]]
 name = "rich"
-version = "10.15.2"
+version = "10.14.0"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 category = "dev"
 optional = false
@@ -893,7 +893,7 @@ test = ["pytest"]
 
 [[package]]
 name = "typed-ast"
-version = "1.5.1"
+version = "1.5.0"
 description = "a fork of Python 2 and 3 ast modules with type comment support"
 category = "dev"
 optional = false
@@ -901,7 +901,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "typing-extensions"
-version = "4.0.1"
+version = "4.0.0"
 description = "Backported and Experimental Type Hints for Python 3.6+"
 category = "main"
 optional = false
@@ -1010,8 +1010,8 @@ certifi = [
     {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
 ]
 charset-normalizer = [
-    {file = "charset-normalizer-2.0.9.tar.gz", hash = "sha256:b0b883e8e874edfdece9c28f314e3dd5badf067342e42fb162203335ae61aa2c"},
+    {file = "charset-normalizer-2.0.8.tar.gz", hash = "sha256:735e240d9a8506778cd7a453d97e817e536bb1fc29f4f6961ce297b9c7a917b0"},
-    {file = "charset_normalizer-2.0.9-py3-none-any.whl", hash = "sha256:1eecaa09422db5be9e29d7fc65664e6c33bd06f9ced7838578ba40d58bdf3721"},
+    {file = "charset_normalizer-2.0.8-py3-none-any.whl", hash = "sha256:83fcdeb225499d6344c8f7f34684c2981270beacc32ede2e669e94f7fa544405"},
 ]
 click = [
     {file = "click-8.0.3-py3-none-any.whl", hash = "sha256:353f466495adaeb40b6b5f592f9f91cb22372351c84caeb068132442a4518ef3"},
@@ -1116,8 +1116,8 @@ iniconfig = [
     {file = "iniconfig-1.1.1.tar.gz", hash = "sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"},
 ]
 ipython = [
-    {file = "ipython-7.30.1-py3-none-any.whl", hash = "sha256:fc60ef843e0863dd4e24ab2bb5698f071031332801ecf8d1aeb4fb622056545c"},
+    {file = "ipython-7.30.0-py3-none-any.whl", hash = "sha256:c8f3e07aefb9cf9e067f39686f035ce09b27a1ee602116a3030b91b6fc138ee4"},
-    {file = "ipython-7.30.1.tar.gz", hash = "sha256:cb6aef731bf708a7727ab6cde8df87f0281b1427d41e65d62d4b68934fa54e97"},
+    {file = "ipython-7.30.0.tar.gz", hash = "sha256:d41f8e80b99690122400f9b2069b12f670246a1b4cc5d332bd6c4e2500e6d6fb"},
 ]
 isodate = [
     {file = "isodate-0.6.0-py2.py3-none-any.whl", hash = "sha256:aa4d33c06640f5352aca96e4b81afd8ab3b47337cc12089822d6f322ac772c81"},
@@ -1226,8 +1226,8 @@ parsedatetime = [
     {file = "parsedatetime-2.4.tar.gz", hash = "sha256:3d817c58fb9570d1eec1dd46fa9448cd644eeed4fb612684b02dfda3a79cb84b"},
 ]
 parso = [
-    {file = "parso-0.8.3-py2.py3-none-any.whl", hash = "sha256:c001d4636cd3aecdaf33cbb40aebb59b094be2a74c556778ef5576c175e19e75"},
+    {file = "parso-0.8.2-py2.py3-none-any.whl", hash = "sha256:a8c4922db71e4fdb90e0d0bc6e50f9b273d3397925e5e60a717e719201778d22"},
-    {file = "parso-0.8.3.tar.gz", hash = "sha256:8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0"},
+    {file = "parso-0.8.2.tar.gz", hash = "sha256:12b83492c6239ce32ff5eed6d3639d6a536170723c6f3f1506869f1ace413398"},
 ]
 pathspec = [
     {file = "pathspec-0.9.0-py2.py3-none-any.whl", hash = "sha256:7d15c4ddb0b5c802d161efc417ec1a2558ea2653c2e8ad9c19098201dc1c993a"},
@@ -1371,8 +1371,8 @@ requests-cache = [
     {file = "requests_cache-0.6.4-py2.py3-none-any.whl", hash = "sha256:1102daa13a804abe23fad62d694e7dee58d6063a35d94bf6e8c9821e22e5a78b"},
 ]
 rich = [
-    {file = "rich-10.15.2-py3-none-any.whl", hash = "sha256:43b2c6ad51f46f6c94992aee546f1c177719f4e05aff8f5ea4d2efae3ebdac89"},
+    {file = "rich-10.14.0-py3-none-any.whl", hash = "sha256:ab9cbfd7a3802d8c6f0fa91e974630e2a69447972dcbb9dfe9b01016dd95e38e"},
-    {file = "rich-10.15.2.tar.gz", hash = "sha256:1dded089b79dd042b3ab5cd63439a338e16652001f0c16e73acdcf4997ad772d"},
+    {file = "rich-10.14.0.tar.gz", hash = "sha256:8bfe4546d56b4131298d3a9e571a0742de342f1593770bd0d4707299f772a0af"},
 ]
 six = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
@@ -1431,29 +1431,29 @@ traitlets = [
     {file = "traitlets-5.1.1.tar.gz", hash = "sha256:059f456c5a7c1c82b98c2e8c799f39c9b8128f6d0d46941ee118daace9eb70c7"},
 ]
 typed-ast = [
-    {file = "typed_ast-1.5.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5d8314c92414ce7481eee7ad42b353943679cf6f30237b5ecbf7d835519e1212"},
+    {file = "typed_ast-1.5.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7b310a207ee9fde3f46ba327989e6cba4195bc0c8c70a158456e7b10233e6bed"},
-    {file = "typed_ast-1.5.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b53ae5de5500529c76225d18eeb060efbcec90ad5e030713fe8dab0fb4531631"},
+    {file = "typed_ast-1.5.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:52ca2b2b524d770bed7a393371a38e91943f9160a190141e0df911586066ecda"},
-    {file = "typed_ast-1.5.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:24058827d8f5d633f97223f5148a7d22628099a3d2efe06654ce872f46f07cdb"},
+    {file = "typed_ast-1.5.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:14fed8820114a389a2b7e91624db5f85f3f6682fda09fe0268a59aabd28fe5f5"},
-    {file = "typed_ast-1.5.1-cp310-cp310-win_amd64.whl", hash = "sha256:a6d495c1ef572519a7bac9534dbf6d94c40e5b6a608ef41136133377bba4aa08"},
+    {file = "typed_ast-1.5.0-cp310-cp310-win_amd64.whl", hash = "sha256:65c81abbabda7d760df7304d843cc9dbe7ef5d485504ca59a46ae2d1731d2428"},
-    {file = "typed_ast-1.5.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:de4ecae89c7d8b56169473e08f6bfd2df7f95015591f43126e4ea7865928677e"},
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-    {file = "typed_ast-1.5.1-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:256115a5bc7ea9e665c6314ed6671ee2c08ca380f9d5f130bd4d2c1f5848d695"},
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+    {file = "typed_ast-1.5.0.tar.gz", hash = "sha256:ff4ad88271aa7a55f19b6a161ed44e088c393846d954729549e3cde8257747bb"},
 ]
 typing-extensions = [
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 ]
 url-normalize = [
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requirements-dev.txt

@@ -9,7 +9,7 @@ babel==2.9.1; python_version >= "2.7" and python_full_version < "3.0.0" or pytho
 backcall==0.2.0; python_version >= "3.7" and python_version < "4.0"
 black==21.11b1; python_full_version >= "3.6.2"
 certifi==2021.10.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
-charset-normalizer==2.0.9; python_full_version >= "3.6.0" and python_version >= "3.6"
+charset-normalizer==2.0.8; python_full_version >= "3.6.0" and python_version >= "3.6"
 click==8.0.3; python_version >= "3.6" and python_full_version >= "3.6.2"
 colorama==0.4.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 commonmark==0.9.1; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")
@@ -24,7 +24,7 @@ greenlet==1.1.2; python_version >= "3" and python_full_version < "3.0.0" or pyth
 idna==3.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
 importlib-metadata==4.8.2; python_full_version >= "3.6.2" and python_version < "3.8" and python_version >= "3.6" 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==7.30.1; python_version >= "3.7" and python_version < "4.0"
+ipython==7.30.0; python_version >= "3.7" and python_version < "4.0"
 isodate==0.6.0
 isort==5.10.1; python_full_version >= "3.6.1" and python_version < "4.0"
 itsdangerous==2.0.1; python_version >= "3.6"
@@ -40,7 +40,7 @@ openpyxl==3.0.9; python_version >= "3.6"
 packaging==21.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 pandas==1.3.4; python_full_version >= "3.7.1"
 parsedatetime==2.4
-parso==0.8.3; python_version >= "3.7" and python_version < "4.0"
+parso==0.8.2; python_version >= "3.7" and python_version < "4.0"
 pathspec==0.9.0; python_full_version >= "3.6.2"
 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"
@@ -65,7 +65,7 @@ pytz==2021.3; python_full_version >= "3.7.1"
 regex==2021.11.10; python_full_version >= "3.6.2"
 requests-cache==0.6.4; python_version >= "3.6"
 requests==2.26.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
-rich==10.15.2; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")
+rich==10.14.0; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")
 six==1.16.0; python_full_version >= "3.7.1" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0")
 spdx-license-list==0.5.2
 sqlalchemy==1.4.22; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
@@ -73,8 +73,8 @@ 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"
 tomli==1.2.2; python_version >= "3.6" and python_full_version >= "3.6.2"
 traitlets==5.1.1; python_version >= "3.7" and python_version < "4.0"
-typed-ast==1.5.1; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.6.2" and python_version >= "3.6"
+typed-ast==1.5.0; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.6.2" and python_version >= "3.6"
-typing-extensions==4.0.1
+typing-extensions==4.0.0
 url-normalize==1.4.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
 urllib3==1.26.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
 wcwidth==0.2.5; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.2"

requirements.txt

@@ -1,5 +1,5 @@
 certifi==2021.10.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
-charset-normalizer==2.0.9; python_full_version >= "3.6.0" and python_version >= "3.6"
+charset-normalizer==2.0.8; python_full_version >= "3.6.0" and 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")
 ftfy==5.9; python_version >= "3.5"
 greenlet==1.1.2; python_version >= "3" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3"
@@ -18,7 +18,7 @@ requests==2.26.0; (python_version >= "2.7" and python_full_version < "3.0.0") or
 six==1.16.0; python_full_version >= "3.7.1" and python_version >= "3.6"
 spdx-license-list==0.5.2
 sqlalchemy==1.4.22; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
-typing-extensions==4.0.1; 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"
+typing-extensions==4.0.0; 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"
 url-normalize==1.4.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
 urllib3==1.26.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
 wcwidth==0.2.5; python_version >= "3.5"

tests/test_check.py

@@ -376,7 +376,7 @@ def test_check_doi_field():
     citation = "Orth, A. 2021. Testing all the things. doi: 10.1186/1743-422X-9-218"
 
     # Emulate a column in a transposed dataframe (which is just a series), with
-    # the citation and a DOI field.
+    # the citation and an empty DOI field.
     d = {"cg.identifier.doi": doi, "dcterms.bibliographicCitation": citation}
     series = pd.Series(data=d)
 
@@ -402,39 +402,3 @@ def test_check_doi_only_in_citation(capsys):
         captured.out
         == f"{Fore.YELLOW}DOI in citation, but missing a DOI field: {Fore.RESET}{citation}\n"
     )
-
-
-def test_title_in_citation():
-    """Test an item with its title in the citation."""
-
-    title = "Testing all the things"
-    citation = "Orth, A. 2021. Testing all the things."
-
-    # Emulate a column in a transposed dataframe (which is just a series), with
-    # the title and citation.
-    d = {"dc.title": title, "dcterms.bibliographicCitation": citation}
-    series = pd.Series(data=d)
-
-    result = check.title_in_citation(series)
-
-    assert result == None
-
-
-def test_title_not_in_citation(capsys):
-    """Test an item with its title missing from the citation."""
-
-    title = "Testing all the things"
-    citation = "Orth, A. 2021. Testing all teh things."
-
-    # Emulate a column in a transposed dataframe (which is just a series), with
-    # the title and citation.
-    d = {"dc.title": title, "dcterms.bibliographicCitation": citation}
-    series = pd.Series(data=d)
-
-    check.title_in_citation(series)
-
-    captured = capsys.readouterr()
-    assert (
-        captured.out
-        == f"{Fore.YELLOW}Title is not present in citation: {Fore.RESET}{title}\n"
-    )