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Merged
robertatakenaka merged 7 commits into from
Nov 21, 2024
Merged

Feat: add person group elem in ref elem #757

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9859915
Adiciona 'node'
Rossi-Luciano Nov 17, 2024
ff33b3f
Adiciona 'docstring'
Rossi-Luciano Nov 17, 2024
8fde0fc
Adiciona'person-group' in 'ref'
Rossi-Luciano Nov 17, 2024
2f7154a
Adiciona teste
Rossi-Luciano Nov 17, 2024
9716dcb
Remove exemplo obsoleto
Rossi-Luciano Nov 17, 2024
89eec1e
Modifica para considerar 'comment'
Rossi-Luciano Nov 20, 2024
6c57af6
Adiciona teste
Rossi-Luciano Nov 20, 2024
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155 changes: 103 additions & 52 deletions packtools/sps/formats/sps_xml/ref.py
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Original file line number Diff line number Diff line change
@@ -1,52 +1,93 @@
"""
data = {
"ref-id": "B1",
"label": "1",
"mixed-citation": "Aires M, Paz AA, Perosa CT. Situação de saúde...",
"publication-type": "journal",
"article-title": "Situação de saúde e grau de...",
"chapter-title": "The epidemiology of idiopathic inflammatory bowel disease.",
"source": "Rev Gaucha Enferm",
"edition": "4th ed",
"publisher-loc": "Rio de Janeiro",
"publisher-name": "Universidade Federal do Paraná",
"volume": "30",
"issue": "3",
"data-title": "Estudos de genes em ratos albinos na América Latina",
"version": "23 jan.",
"series": "Second International Workshop",
"day": "22",
"month": "10",
"year": "2009",
"fpage": "192",
"lpage": "199",
"ext-link": [
{
"ext-link-type": "uri",
"xlink:href": "http://socialsciences.scielo.org",
"text": "http://socialsciences.scielo.org"
}
]
"pub-ids": [
{
"pub-id-type": "pmid",
"text": "15867408"
}
]
"dates-in-citation": [
{
"content-type": "updated",
"text": "2006 Jul 20"
}
]
}

"""

import xml.etree.ElementTree as ET


def build_ref(data):
def build_ref(data, node=None):
"""
Builds an XML element representing a bibliographic reference.

Args:
data (dict): A dictionary containing reference details with the following structure:
- "ref-id" (str): Unique identifier for the reference (required).
- "label" (str): Label for the reference, e.g., "1" (optional).
- "mixed-citation" (str): Mixed content citation text (optional).
- "publication-type" (str): Type of publication, e.g., "journal", "book" (required).
- Additional bibliographic keys (optional):
- "article-title", "chapter-title", "source", "edition", "publisher-loc",
"publisher-name", "series", "day", "month", "year", "volume", "issue",
"data-title", "version", "fpage", "lpage".
- "ext-link" (list): A list of dictionaries, each containing:
- "ext-link-type" (str): Type of external link (e.g., "uri") (required).
- "xlink:href" (str): URL or URI of the external link (required).
- "text" (str): Display text for the link (optional).
- "pub-ids" (list): A list of dictionaries, each containing:
- "pub-id-type" (str): Type of publication ID (e.g., "pmid") (required).
- "text" (str): Value of the publication ID (required).
- "dates-in-citation" (list): A list of dictionaries, each containing:
- "content-type" (str): Type of date, e.g., "updated" (required).
- "text" (str): Date value in text format (required).
node (dict, optional): A dictionary containing additional XML elements to include in
the reference. For example:
- "person-group" (list): A list of XML elements representing authors or editors.

Returns:
xml.etree.ElementTree.Element: An XML element representing the reference.

Raises:
ValueError: If required fields are missing, including:
- "ref-id".
- "publication-type".
- "ext-link-type" and "xlink:href" for external links.
- "pub-id-type" for publication IDs.
- "content-type" for dates in citation.

Example input:
data = {
"ref-id": "B1",
"label": "1",
"mixed-citation": "Aires M, Paz AA, Perosa CT. Situação de saúde...",
"publication-type": "journal",
"article-title": "Situação de saúde e grau de...",
"source": "Rev Gaucha Enferm",
"volume": "30",
"issue": "3",
"fpage": "192",
"lpage": "199",
"ext-link": [
{
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@robertatakenaka robertatakenaka Nov 19, 2024 •
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@Rossi-Luciano considere adicionar <comment/>

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@Rossi-Luciano Rossi-Luciano Nov 20, 2024

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OK, @robertatakenaka

"comment": "Disponível em: ",
"ext-link-type": "uri",
"xlink:href": "http://example.com",
"text": "http://example.com"
}
],
"pub-ids": [
{
"pub-id-type": "pmid",
"text": "12345678"
}
]
}
node = {
"person-group": [ET.Element("person-group", attrib={"person-group-type": "author"})]
}

Example output:
<ref id="B1">
<label>1</label>
<mixed-citation>Aires M, Paz AA, Perosa CT. Situação de saúde...</mixed-citation>
<element-citation publication-type="journal">
<article-title>Situação de saúde e grau de...</article-title>
<source>Rev Gaucha Enferm</source>
<volume>30</volume>
<issue>3</issue>
<fpage>192</fpage>
<lpage>199</lpage>
<ext-link ext-link-type="uri" xlink:href="http://example.com">http://example.com</ext-link>
<pub-id pub-id-type="pmid">12345678</pub-id>
<person-group person-group-type="author" />
</element-citation>
</ref>
"""
if not (id_text := data.get("ref-id")):
raise ValueError("attribute ref-id is required")

Expand All @@ -63,6 +104,10 @@ def build_ref(data):
ref_elem, "element-citation", attrib={"publication-type": publication_type}
)

if node:
for person_group in node.get("person-group") or []:
element_citation_elem.append(person_group)

basic_keys = (
"article-title",
"chapter-title",
Expand Down Expand Up @@ -92,12 +137,18 @@ def build_ref(data):
if not ext_link_type or not xlink_href:
raise ValueError("ext-link-type and xlink:href are required")

if ext_link_text := ext_link.get("text"):
ET.SubElement(
element_citation_elem,
"ext-link",
attrib={"ext-link-type": ext_link_type, "xlink:href": xlink_href},
).text = ext_link_text
ext_link_text = ext_link.get("text")
comment = ext_link.get("comment")

if ext_link_text:
ext_link_attributes = {"ext-link-type": ext_link_type, "xlink:href": xlink_href}

if comment:
comment_elem = ET.SubElement(element_citation_elem, "comment")
comment_elem.text = comment
ET.SubElement(comment_elem, "ext-link", attrib=ext_link_attributes).text = ext_link_text
else:
ET.SubElement(element_citation_elem, "ext-link", attrib=ext_link_attributes).text = ext_link_text

for pub_id in data.get("pub-ids") or []:
pub_id_type = pub_id.get("pub-id-type")
Expand Down
66 changes: 66 additions & 0 deletions tests/sps/formats/sps_xml/test_ref.py
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,33 @@ def test_build_ref_ext_link_text_None(self):
generated_xml_str = ET.tostring(ref_elem, encoding="unicode", method="xml")
self.assertEqual(generated_xml_str.strip(), expected_xml_str.strip())

def test_build_ref_ext_link_in_comment(self):
self.maxDiff = None
data = {
"ref-id": "B1",
"publication-type": "journal",
"ext-link": [
{
"ext-link-type": "uri",
"xlink:href": "http://socialsciences.scielo.org",
"text": "http://socialsciences.scielo.org",
"comment": "Disponível em: "
}
]
}
expected_xml_str = (
'<ref id="B1">'
'<element-citation publication-type="journal">'
'<comment>'
'Disponível em: <ext-link ext-link-type="uri" xlink:href="http://socialsciences.scielo.org">http://socialsciences.scielo.org</ext-link>'
'</comment>'
'</element-citation>'
'</ref>'
)
ref_elem = build_ref(data)
generated_xml_str = ET.tostring(ref_elem, encoding="unicode", method="xml")
self.assertEqual(generated_xml_str.strip(), expected_xml_str.strip())


class TestBuildRefPubId(unittest.TestCase):
def test_build_ref_pub_id(self):
Expand Down Expand Up @@ -319,3 +346,42 @@ def test_build_ref_date_in_citation_text_None(self):
ref_elem = build_ref(data)
generated_xml_str = ET.tostring(ref_elem, encoding="unicode", method="xml")
self.assertEqual(generated_xml_str.strip(), expected_xml_str.strip())


class TestBuildRefPersonGroup(unittest.TestCase):
def test_build_ref_person_group(self):
data = {
"ref-id": "B1",
"publication-type": "journal",
}
node = {
"person-group": [
ET.fromstring(
'<person-group person-group-type="author">'
'<name>'
'<surname>Einstein</surname>'
'<given-names>Albert</given-names>'
'<prefix>Prof.</prefix>'
'<suffix>Neto</suffix>'
'</name>'
'</person-group>'
)
]
}
expected_xml_str = (
'<ref id="B1">'
'<element-citation publication-type="journal">'
'<person-group person-group-type="author">'
'<name>'
'<surname>Einstein</surname>'
'<given-names>Albert</given-names>'
'<prefix>Prof.</prefix>'
'<suffix>Neto</suffix>'
'</name>'
'</person-group>'
'</element-citation>'
'</ref>'
)
ref_elem = build_ref(data, node)
generated_xml_str = ET.tostring(ref_elem, encoding="unicode", method="xml")
self.assertEqual(generated_xml_str.strip(), expected_xml_str.strip())