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authorBryan Newbold <bnewbold@robocracy.org>2019-03-05 18:42:43 -0800
committerBryan Newbold <bnewbold@robocracy.org>2019-05-21 11:41:29 -0700
commitee393b537f3164ad25c9337b658db81192b25629 (patch)
treec1962719963942d56b8194694567d25b03dc4f5b /python
parenta987af927686725f7778475f4c383d59c8c494bf (diff)
downloadfatcat-ee393b537f3164ad25c9337b658db81192b25629.tar.gz
fatcat-ee393b537f3164ad25c9337b658db81192b25629.zip
basic JSTOR XML parser
Diffstat (limited to 'python')
-rw-r--r--python/parse_jstor_xml.py177
-rw-r--r--python/tests/files/jstor-article-10.2307_111039.xml58
2 files changed, 235 insertions, 0 deletions
diff --git a/python/parse_jstor_xml.py b/python/parse_jstor_xml.py
new file mode 100644
index 00000000..dfb899fd
--- /dev/null
+++ b/python/parse_jstor_xml.py
@@ -0,0 +1,177 @@
+
+import sys
+import json
+import datetime
+from bs4 import BeautifulSoup
+from bs4.element import NavigableString
+
+
+class JstorXmlParser():
+ """
+ Converts JSTOR bulk XML metadata (eg, from their Early Journals Collection)
+ """
+
+ def __init__(self):
+ pass
+
+ def parse_file(self, handle):
+
+ # 1. open with beautiful soup
+ soup = BeautifulSoup(handle, "xml")
+
+ # 2. iterate over articles, call parse_article on each
+ for article in soup.find_all("article"):
+ resp = self.parse_article(article)
+ print(json.dumps(resp))
+ #sys.exit(-1)
+
+ def parse_article(self, article):
+
+ journal_meta = article.front.find("journal-meta")
+ article_meta = article.front.find("article-meta")
+
+ extra = dict()
+ extra_jstor = dict()
+
+ journal_title = journal_meta.find("journal-title").string
+ publisher = journal_meta.find("publisher-name").string
+ issn = journal_meta.find("issn")
+ if issn:
+ issn = issn.string
+ if len(issn) == 8:
+ issn = "{}-{}".format(issn[0:4], issn[4:8])
+ else:
+ assert len(issn) == 9
+ container = dict(
+ name=journal_title,
+ publisher=publisher,
+ issn=issn, # TODO: ISSN-L lookup...
+ )
+
+ doi = article_meta.find("article-id", attr={"pub-id-type": "doi"})
+ if doi:
+ doi = doi.string.lower().strip()
+
+ title = article_meta.find("article-title")
+ if title:
+ title = title.string.strip()
+ if title.endswith('.'):
+ title = title[:-1]
+
+ contribs = []
+ cgroup = article_meta.find("contrib-group")
+ if cgroup:
+ for c in cgroup.find_all("contrib"):
+ given = c.find("given-names")
+ surname = c.find("surname")
+ if given and surname:
+ name = "{} {}".format(given.string, surname.string)
+ elif surname:
+ name = surname.string
+ else:
+ name = None
+ contribs.append(dict(
+ role=c['contrib-type'], # XXX: types? mapping?
+ raw_name=name,
+ ))
+
+ release_year = None
+ release_date = None
+ pub_date = article_meta.find('pub-date')
+ if pub_date and pub_date.year:
+ release_year = int(pub_date.year.string)
+ if pub_date.month and pub_date.day:
+ release_date = datetime.date(
+ release_year,
+ int(pub_date.month.string),
+ int(pub_date.day.string))
+
+ volume = None
+ if article_meta.volume:
+ volume = article_meta.volume.string or None
+
+ issue = None
+ if article_meta.issue:
+ issue = article_meta.issue.string or None
+
+ pages = None
+ if article_meta.find("page-range"):
+ pages = article_meta.find("page-range").string
+ elif article_meta.fpage:
+ pages = article_meta.fpage.string
+
+ language = None
+ cm = article_meta.find("custom-meta")
+ if cm.find("meta-name").string == "lang":
+ language = cm.find("meta-value").string
+
+ release_type = "article-journal"
+ if "[Abstract]" in title:
+ release_type = "abstract"
+ elif "[Editorial" in title:
+ release_type = "editorial"
+ elif "[Letter" in title:
+ release_type = "letter"
+ elif "[Poem" in title or "[Photograph" in title:
+ release_type = None
+ else if title.startswith("[") and title.endswith("]"):
+ # strip brackets if that is all that is there (eg, translation or non-english)
+ title = title[1:-1]
+
+ # everything in JSTOR is published
+ release_status = "published"
+
+ if extra_jstor:
+ extra['jstor'] = extra_jstor
+ if not extra:
+ extra = None
+
+ re = dict(
+ issn=issn, # not an entity field
+ #work_id
+ title=title,
+ #original_title
+ release_type=release_type,
+ release_status=release_status,
+ release_date=release_date.isoformat(),
+ release_year=release_year,
+ doi=doi,
+ #pmid
+ #pmcid
+ #isbn13 # TODO: ?
+ volume=volume,
+ issue=issue,
+ pages=pages,
+ publisher=publisher,
+ language=language,
+ #license_slug # TODO: ?
+
+ # content, mimetype, lang
+ #abstracts=abstracts,
+
+ # raw_name, role, raw_affiliation, extra
+ contribs=contribs,
+
+ # key, year, container_name, title, locator
+ # extra: volume, authors, issue, publisher, identifiers
+ #refs=refs,
+
+ # name, type, publisher, issnl
+ # extra: issnp, issne, original_name, languages, country
+ container=container,
+
+ # extra:
+ # withdrawn_date
+ # translation_of
+ # subtitle
+ # aliases
+ # container_name
+ # group-title
+ # pubmed: retraction refs
+ extra=extra,
+ )
+ return re
+
+if __name__=='__main__':
+ parser = JstorXmlParser()
+ parser.parse_file(open(sys.argv[1]))
diff --git a/python/tests/files/jstor-article-10.2307_111039.xml b/python/tests/files/jstor-article-10.2307_111039.xml
new file mode 100644
index 00000000..1a4c760d
--- /dev/null
+++ b/python/tests/files/jstor-article-10.2307_111039.xml
@@ -0,0 +1,58 @@
+<article xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns:mml="http://www.w3.org/1998/Math/MathML"
+ dtd-version="1.0"
+ article-type="research-article">
+ <front>
+ <journal-meta>
+ <journal-id journal-id-type="jstor">abstpapecommroya</journal-id>
+ <journal-id journal-id-type="jstor">j100687</journal-id>
+ <journal-title-group>
+ <journal-title>Abstracts of the Papers Communicated to the Royal Society of London</journal-title>
+ </journal-title-group>
+ <publisher>
+ <publisher-name>The Royal Society</publisher-name>
+ </publisher>
+ <issn pub-type="ppub">03650855</issn>
+ </journal-meta>
+ <article-meta>
+ <article-id pub-id-type="jstor">111039</article-id>
+ <title-group>
+ <article-title>On the Universal Law of Attraction, Including that of Gravitation, as a Particular Case of Approximation Deducible from the Principle that Equal and Similar Particles of Matter Move Similarly, Relatively to Each other. [Abstract]</article-title>
+ </title-group>
+ <contrib-group>
+ <contrib contrib-type="author">
+ <string-name>
+ <given-names>John Kinnersley</given-names>
+ <surname>Smythies</surname>
+ </string-name>
+ </contrib>
+ </contrib-group>
+ <pub-date>
+ <day>1</day>
+ <month>1</month>
+ <year>1843</year>
+
+ <day>1</day>
+ <month>1</month>
+ <year>1850</year>
+ </pub-date>
+ <volume>5</volume>
+ <issue/>
+ <issue-id>i207047</issue-id>
+ <fpage>831</fpage>
+ <lpage>832</lpage>
+ <page-range>831-832</page-range>
+ <permissions>
+ <copyright-statement/>
+ </permissions>
+ <self-uri xlink:href="http://www.jstor.org/stable/111039"/>
+ <custom-meta-group>
+ <custom-meta>
+ <meta-name>lang</meta-name>
+ <meta-value>eng</meta-value>
+ </custom-meta>
+ </custom-meta-group>
+ </article-meta>
+ </front>
+</article>