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feat(pubmed): implementar CopyrightInformation e CoiStatement #1247

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feat(pubmed): implementar CopyrightInformation e CoiStatement #1247

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37 changes: 29 additions & 8 deletions packtools/sps/formats/pubmed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
journal_meta,
kwd_group,
)
from packtools.sps.utils.xml_utils import node_plain_text


def xml_pubmed_article_pipe():
Expand Down Expand Up @@ -508,18 +509,38 @@ def xml_pubmed_history(xml_pubmed, xml_tree):
xml_pubmed.append(history)


def get_copyright_information(xml_tree):
copyright_statement = xml_tree.find(".//permissions/copyright-statement")
return node_plain_text(copyright_statement) or None


def xml_pubmed_copyright_information(xml_pubmed, xml_tree):
...
# TODO
# The Copyright information associated with this article.
# There is no example of using this value in the files.
"""
<CopyrightInformation>Copyright © 2023 The Authors</CopyrightInformation>
"""
copyright_information = get_copyright_information(xml_tree)
if copyright_information:
el = ET.Element("CopyrightInformation")
el.text = copyright_information
xml_pubmed.append(el)


def get_coi_statement(xml_tree):
fn_node = xml_tree.find('.//fn[@fn-type="coi-statement"]')
if fn_node is None:
return None
return node_plain_text(fn_node.find("p")) or node_plain_text(fn_node) or None


def xml_pubmed_coi_statement(xml_pubmed, xml_tree):
...
# TODO
# The Conflict of Interest statement associated with this article.
# There is no example of using this value in the files.
"""
<CoiStatement>Não há conflito de interesse entre os autores do artigo.</CoiStatement>
"""
coi_statement = get_coi_statement(xml_tree)
if coi_statement:
el = ET.Element("CoiStatement")
el.text = coi_statement
xml_pubmed.append(el)


def get_keywords(xml_tree):
Expand Down
115 changes: 115 additions & 0 deletions tests/sps/formats/test_pubmed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
xml_pubmed_publication_type,
xml_pubmed_article_id,
xml_pubmed_history,
xml_pubmed_copyright_information,
xml_pubmed_coi_statement,
xml_pubmed_vernacular_title_pipe,
xml_pubmed_object_list,
xml_pubmed_title_reference_list,
Expand Down Expand Up @@ -1243,6 +1245,119 @@ def test_xml_pubmed_history(self):

self.assertEqual(obtained, expected)

def test_xml_pubmed_copyright_information(self):
expected = (
'<Article>'
'<CopyrightInformation>Copyright © 2023 The Authors</CopyrightInformation>'
'</Article>'
)
xml_pubmed = ET.fromstring(
'<Article/>'
)
xml_tree = ET.fromstring(
'<article xmlns:mml="http://www.w3.org/1998/Math/MathML" '
'xmlns:xlink="http://www.w3.org/1999/xlink" '
'article-type="research-article" dtd-version="1.1" specific-use="sps-1.9" xml:lang="en">'
'<front>'
'<article-meta>'
'<permissions>'
'<copyright-statement>Copyright © 2023 The Authors</copyright-statement>'
'</permissions>'
'</article-meta>'
'</front>'
'</article>'
)

xml_pubmed_copyright_information(xml_pubmed, xml_tree)

obtained = ET.tostring(xml_pubmed, encoding="utf-8").decode("utf-8")

self.assertEqual(obtained, expected)

def test_xml_pubmed_copyright_information_without_statement(self):
expected = (
'<Article/>'
)
xml_pubmed = ET.fromstring(
'<Article/>'
)
xml_tree = ET.fromstring(
'<article xmlns:mml="http://www.w3.org/1998/Math/MathML" '
'xmlns:xlink="http://www.w3.org/1999/xlink" '
'article-type="research-article" dtd-version="1.1" specific-use="sps-1.9" xml:lang="en">'
'<front>'
'<article-meta>'
'<permissions>'
'</permissions>'
'</article-meta>'
'</front>'
'</article>'
)

xml_pubmed_copyright_information(xml_pubmed, xml_tree)

obtained = ET.tostring(xml_pubmed, encoding="utf-8").decode("utf-8")

self.assertEqual(obtained, expected)

def test_xml_pubmed_coi_statement(self):
expected = (
'<Article>'
'<CoiStatement>Não há conflito de interesse entre os autores do artigo.</CoiStatement>'
'</Article>'
)
xml_pubmed = ET.fromstring(
'<Article/>'
)
xml_tree = ET.fromstring(
'<article xmlns:mml="http://www.w3.org/1998/Math/MathML" '
'xmlns:xlink="http://www.w3.org/1999/xlink" '
'article-type="research-article" dtd-version="1.1" specific-use="sps-1.9" xml:lang="pt">'
'<front>'
'<article-meta>'
'<author-notes>'
'<fn fn-type="coi-statement">'
'<label>Conflito de Interesses</label>'
'<p>Não há conflito de interesse entre os autores do artigo.</p>'
'</fn>'
'</author-notes>'
'</article-meta>'
'</front>'
'</article>'
)

xml_pubmed_coi_statement(xml_pubmed, xml_tree)

obtained = ET.tostring(xml_pubmed, encoding="utf-8").decode("utf-8")

self.assertEqual(obtained, expected)

def test_xml_pubmed_coi_statement_without_fn(self):
expected = (
'<Article/>'
)
xml_pubmed = ET.fromstring(
'<Article/>'
)
xml_tree = ET.fromstring(
'<article xmlns:mml="http://www.w3.org/1998/Math/MathML" '
'xmlns:xlink="http://www.w3.org/1999/xlink" '
'article-type="research-article" dtd-version="1.1" specific-use="sps-1.9" xml:lang="en">'
'<front>'
'<article-meta>'
'<author-notes>'
'</author-notes>'
'</article-meta>'
'</front>'
'</article>'
)

xml_pubmed_coi_statement(xml_pubmed, xml_tree)

obtained = ET.tostring(xml_pubmed, encoding="utf-8").decode("utf-8")

self.assertEqual(obtained, expected)

def test_xml_pubmed_object_list_keyword(self):
expected = (
'<Article>'
Expand Down