BibTeX in Python

Tutorial/01 SQLite in Python/__main__.py

@@ -1,7 +1,7 @@
 from sqlite3 import connect
 
 class DB:
-	def __init__(self,path="example/people.db"):
+	def __init__(self,path="people.db"):
 		self.conn = connect(path)
 		self.c = self.conn.cursor()
 

Tutorial/01 SQLite in Python/sql_fill.py

@@ -1,9 +1,8 @@
 import sqlite3
 
-conn = sqlite3.connect('example/people.db')
+conn = sqlite3.connect('people.db')
 c = conn.cursor()
 
-c.execute("DROP TABLE people")
 c.execute("CREATE TABLE people (orcid CHARACTER(16), start DATE, end DATE)")
 c.execute("INSERT INTO people VALUES ('0000000219094153','1900-01-01','2016-12-31')")
 c.execute("INSERT INTO people VALUES ('000000020183570X','1900-01-01','2016-12-31')")

Tutorial/02 DATE, ORCID and WorkSummary Class(Filter 1)/__main__.py

@@ -1,7 +1,7 @@
 from sqlite3 import connect
 
 class DB:
-	def __init__(self,path="example/people.db"):
+	def __init__(self,path="people.db"):
 		self.conn = connect(path)
 		self.c = self.conn.cursor()
 

Tutorial/03 Rest API/__main__.py

@@ -1,7 +1,7 @@
 from sqlite3 import connect
 
 class DB:
-	def __init__(self,path="example/people.db"):
+	def __init__(self,path="people.db"):
 		self.conn = connect(path)
 		self.c = self.conn.cursor()
 

Tutorial/04 Sorting and Filter 2/__main__.py

@@ -1,7 +1,7 @@
 from sqlite3 import connect
 
 class DB:
-	def __init__(self,path="example/people.db"):
+	def __init__(self,path="people.db"):
 		self.conn = connect(path)
 		self.c = self.conn.cursor()
 

Tutorial/05 BibTeX in Python/__main__.py

@@ -0,0 +1,209 @@
+from sqlite3 import connect
+
+class DB:
+	def __init__(self,path="people.db"):
+		self.conn = connect(path)
+		self.c = self.conn.cursor()
+
+	def getList(self):
+		self.c.execute('SELECT * FROM people')
+		return self.c.fetchall()
+
+	def close(self):
+		self.conn.close()
+
+class Date:
+	def __init__(self, y, m, d):
+		self.y = int(y)
+		self.m = int(m) if m else None
+		self.d = int(d) if d else None
+	def check (self, other, attr):
+		if getattr(self,attr) == None or getattr(other,attr) == None:
+			return 1
+		if getattr(self,attr) < getattr(other,attr):
+			return 1
+		if getattr(self,attr) > getattr(other,attr):
+			return -1
+		return 0
+	__le__ = lambda self, other: True if 1 == (self.check(other,"y") or self.check(other,"m") or self.check(other,"d") or 1) else False
+	__str__ = lambda self: str(self.y) + "-" + str(self.m) + "-" + str(self.d)
+
+class OrcID:
+	def __init__(self, id, start, stop):
+		self.id = id
+		self.start = Date(*start.split("-"))
+		self.stop = Date(*stop.split("-"))
+	getID = lambda self: "-".join([self.id[4 * i : 4 * (i + 1)]  for i in range(4)])
+	__str__ = lambda self: self.getID() + ": " + str(self.start) + " - " + str(self.stop)
+
+class WorkSummary:
+	def __init__(self, path, title, date):
+		self.path = path
+		self.title = title
+		self.date = date
+	__lt__ = lambda self, other: self.date.y < other.date.y or (self.date.y == other.date.y and self.title < other.title)
+	__eq__ = lambda self, other: self.date.y == other.date.y and self.title == other.title
+	__str__ = lambda self: self.title + ": " + str(self.date)
+
+from requests import Session
+class API:
+	auth = "https://sandbox.orcid.org/oauth/token"
+	ORC_client_id = "APP-DZ4II2NELOUB89VC"
+	ORC_client_secret = "c0a5796e-4ed3-494b-987e-827755174718"
+	def __init__(self):
+		self.s = Session()
+		self.s.headers = {'Accept': 'application/json'}
+		data = {"grant_type":"client_credentials", "scope":"/read-public","client_id":self.ORC_client_id, "client_secret":self.ORC_client_secret}
+		r = self.s.request(method ="post",url= self.auth, data=data)
+		self.s.headers = {'Accept': 'application/json', "Access token":r.json()["access_token"]}
+	baseurl = "https://pub.sandbox.orcid.org/v2.0"
+	getDate = lambda self,d: Date(d["year"]["value"],d["month"]["value"] if d["month"] else None, d["day"]["value"] if d["day"] else None )
+	def getWorks(self,id):
+		r = self.s.request(method= "get",url = "{0}/{1}/works".format( self.baseurl, id.getID()))
+		for work in (w["work-summary"][0] for w in r.json()["group"]):
+			yield WorkSummary(work["path"],work["title"]["title"]["value"],self.getDate(work["publication-date"]))
+	def getWork(self, summary):
+		r = self.s.request(method= "get",url= self.baseurl + summary.path)
+		return r.json()['citation']['citation-value']
+
+import itertools
+
+from pybtex.database import parse_string, BibliographyData
+def joinBibliography(bib1, bib2):
+	for key in bib2.entries:
+		bib1.entries[key] = bib2.entries[key]
+
+#if __name__ == "__main__":
+#	db = DB()
+#	orcs = [OrcID(*t) for t in db.getList()]
+#	db.close()
+#	alldocs = []
+#	api = API()
+#	for orc in orcs:
+#		alldocs += [d for d in api.getWorks(orc) if orc.start <= d.date <= orc.stop]
+#	alldocs.sort()
+#	uniqdocs = [doc for doc,_ in itertools.groupby(alldocs)]
+#	bib = BibliographyData()
+#	for d in uniqdocs:
+#		joinBibliography (bib,parse_string(api.getWork(d),"bibtex"))
+#	bib.to_file(open("out.bib","w"))
+
+from pybtex.style.formatting.unsrt import Style
+from pybtex.backends.html import Backend
+#if __name__ == "__main__":
+#	db = DB()
+#	orcs = [OrcID(*t) for t in db.getList()]
+#	db.close()
+#	alldocs = []
+#	api = API()
+#	for orc in orcs:
+#		alldocs += [d for d in api.getWorks(orc) if orc.start <= d.date <= orc.stop]
+#	alldocs.sort()
+#	uniqdocs = [doc for doc,_ in itertools.groupby(alldocs)]
+#	bib = BibliographyData()
+#	for d in uniqdocs:
+#		joinBibliography (bib,parse_string(api.getWork(d),"bibtex"))
+#	style = Style()
+#	formatbib = style.format_bibliography(bib)
+#	back = Backend()
+#	back.write_to_file(formatbib,"out.html")
+
+
+from pybtex.richtext import Tag,Text,Symbol,HRef
+
+class HtmlTag(Tag):
+	def __init__(self, name, opt, *args):
+		super(HtmlTag,self).__init__(name, *args)
+		self.options = opt
+	def render(self, backend):
+		text = super(Tag, self).render(backend)
+		try:
+			return backend.format_tag(self.name, text, self.options)
+		except TypeError:
+			return backend.format_tag(self.name, text)
+
+class HtmlStyle(Style):
+	def format_article(self, context):
+		ret = Text()
+		ret += HtmlTag("h4","style=\"margin-bottom: 2px;\"", context.rich_fields['title'])
+		ret += Tag("i",context.rich_fields['author']) + Symbol('newblock')
+		ret += context.rich_fields['journal']
+		if 'volume' in context.fields:
+			ret += Symbol("nbsp") + context.rich_fields['volume']
+		if 'number' in context.fields:
+			ret += Symbol("nbsp") + "(" + context.rich_fields['number'] + ")"
+		if 'pages' in context.fields:
+			ret = ret + ":" + context.rich_fields['pages']
+		if 'doi' in context.fields:
+			ret += Symbol('newblock') + HRef('https://doi.org/' + context.fields['doi'],"[ Publishers's page ]")
+		return HtmlTag("div","class=\"" + context.fields['year'] +  " mix \"",ret)
+
+#if __name__ == "__main__":
+#	db = DB()
+#	orcs = [OrcID(*t) for t in db.getList()]
+#	db.close()
+#	alldocs = []
+#	api = API()
+#	for orc in orcs:
+#		alldocs += [d for d in api.getWorks(orc) if orc.start <= d.date <= orc.stop]
+#	alldocs.sort()
+#	uniqdocs = [doc for doc,_ in itertools.groupby(alldocs)]
+#	bib = BibliographyData()
+#	for d in uniqdocs:
+#		joinBibliography (bib,parse_string(api.getWork(d),"bibtex"))
+#	style = HtmlStyle()
+#	style.sort = lambda x: sorted(x, key = lambda e:-int(e.fields['year']))
+#	formatbib = style.format_bibliography(bib)
+#	back = Backend()
+#	back.write_to_file(formatbib,"out.html")
+
+class HtmlBackend(Backend):
+	symbols = {'ndash': u'&ndash;', 'newblock': u'<br/>\n', 'nbsp': u'&nbsp;'}
+	format_tag = lambda self, tag, text, options =None: u'<{0} {2} >{1}</{0}>'.format(tag, text, options if options else "") if text else u''
+	label = None
+	def write_entry(self, key, label, text):
+		if label != self.label:
+			self.output(u'<h3 class=\"{0} year\">{0}</h3>\n'.format(label))
+			self.label = label
+		self.output(u'%s\n' % text)
+	write_epilogue = lambda self: self.output(u'</div></body></html>\n')
+	prologue = u"""<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN">
+		<html>
+		<head><meta name="generator" content="Pybtex">
+		<meta http-equiv="Content-Type" content="text/html; charset=%s">
+		<title>Bibliography</title>
+		{HEAD}
+		</head>
+		<body>
+		{BODY}
+		<div id="content">
+		"""
+	def prepout (self, head, body):
+		self.prologue = self.prologue.format(HEAD = head, BODY = body)
+	def write_prologue(self):
+		try:
+			self.prepout("","")
+		except ValueError:
+			pass
+		self.output(self.prologue % (self.encoding or pybtex.io.get_default_encoding()))
+
+
+if __name__ == "__main__":
+	db = DB()
+	orcs = [OrcID(*t) for t in db.getList()]
+	db.close()
+	alldocs = []
+	api = API()
+	for orc in orcs:
+		alldocs += [d for d in api.getWorks(orc) if orc.start <= d.date <= orc.stop]
+	alldocs.sort()
+	uniqdocs = [doc for doc,_ in itertools.groupby(alldocs)]
+	bib = BibliographyData()
+	for d in uniqdocs:
+		joinBibliography (bib,parse_string(api.getWork(d),"bibtex"))
+	style = HtmlStyle()
+	style.sort = lambda x: sorted(x, key = lambda e:-int(e.fields['year']))
+	style.format_labels =  lambda x: [int(e.fields['year']) for e in x]
+	formatbib = style.format_bibliography(bib)
+	back = HtmlBackend()
+	back.write_to_file(formatbib,"out.html")

Tutorial/05 BibTeX in Python/out.bib

@@ -0,0 +1,62 @@
+@article{micceri1989unicorn,
+    author = "Micceri, Theodore",
+    title = "The unicorn, the normal curve, and other improbable creatures.",
+    journal = "Psychological bulletin",
+    volume = "105",
+    number = "1",
+    pages = "156",
+    year = "1989",
+    publisher = "American Psychological Association"
+}
+
+@article{barthes199411,
+    author = "Barthes, Roland",
+    title = "11 The Death of the Author",
+    journal = "Media Texts, Authors and Readers: A Reader",
+    pages = "166",
+    year = "1994",
+    publisher = "Multilingual Matters"
+}
+
+@article{collins1998s,
+    author = "Collins, James J and Chow, Carson C",
+    title = "It's a small world",
+    journal = "Nature",
+    volume = "393",
+    number = "6684",
+    pages = "409--410",
+    year = "1998",
+    publisher = "Nature Publishing Group"
+}
+
+@article{curtiss2013unicorn,
+    author = "Curtiss, Michael and Becker, Iain and Bosman, Tudor and Doroshenko, Sergey and Grijincu, Lucian and Jackson, Tom and Kunnatur, Sandhya and Lassen, Soren and Pronin, Philip and Sankar, Sriram and others",
+    title = "Unicorn: A system for searching the social graph",
+    journal = "Proceedings of the VLDB Endowment",
+    volume = "6",
+    number = "11",
+    pages = "1150--1161",
+    year = "2013",
+    publisher = "VLDB Endowment",
+    doi = "10.14778/2536222.2536239"
+}
+
+@article{aad2015combined,
+    author = "Aad, Georges and Abbott, B and Abdallah, J and Abdinov, O and Aben, R and Abolins, M and AbouZeid, OS and Abramowicz, H and Abreu, H and Abreu, R and others",
+    title = "Combined Measurement of the Higgs Boson Mass in p p Collisions at s= 7 and 8 TeV with the ATLAS and CMS Experiments",
+    journal = "Physical review letters",
+    volume = "114",
+    number = "19",
+    pages = "191803",
+    year = "2015",
+    publisher = "APS"
+}
+
+@article{cheng2015generalized,
+    author = "Cheng, Xinyue and Zou, Yangyang",
+    title = "The generalized unicorn problem in Finsler geometry",
+    journal = "Differential Geometry-Dynamical Systems",
+    volume = "17",
+    pages = "38--48",
+    year = "2015"
+}

Tutorial/05 BibTeX in Python/out_1.html

@@ -0,0 +1,34 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN">
+<html>
+<head><meta name="generator" content="Pybtex">
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Bibliography</title>
+</head>
+<body>
+<dl>
+<dt>1</dt>
+<dd>Theodore Micceri.
+The unicorn, the normal curve, and other improbable creatures.
+<em>Psychological bulletin</em>, 105(1):156, 1989.</dd>
+<dt>2</dt>
+<dd>Roland Barthes.
+11 the death of the author.
+<em>Media Texts, Authors and Readers: A Reader</em>, pages 166, 1994.</dd>
+<dt>3</dt>
+<dd>James&nbsp;J Collins and Carson&nbsp;C Chow.
+It's a small world.
+<em>Nature</em>, 393(6684):409–410, 1998.</dd>
+<dt>4</dt>
+<dd>Michael Curtiss, Iain Becker, Tudor Bosman, Sergey Doroshenko, Lucian Grijincu, Tom Jackson, Sandhya Kunnatur, Soren Lassen, Philip Pronin, Sriram Sankar, and others.
+Unicorn: a system for searching the social graph.
+<em>Proceedings of the VLDB Endowment</em>, 6(11):1150–1161, 2013.
+<a href="https://doi.org/10.14778/2536222.2536239">doi:10.14778/2536222.2536239</a>.</dd>
+<dt>5</dt>
+<dd>Georges Aad, B&nbsp;Abbott, J&nbsp;Abdallah, O&nbsp;Abdinov, R&nbsp;Aben, M&nbsp;Abolins, OS&nbsp;AbouZeid, H&nbsp;Abramowicz, H&nbsp;Abreu, R&nbsp;Abreu, and others.
+Combined measurement of the higgs boson mass in p p collisions at s= 7 and 8 tev with the atlas and cms experiments.
+<em>Physical review letters</em>, 114(19):191803, 2015.</dd>
+<dt>6</dt>
+<dd>Xinyue Cheng and Yangyang Zou.
+The generalized unicorn problem in finsler geometry.
+<em>Differential Geometry-Dynamical Systems</em>, 17:38–48, 2015.</dd>
+</dl></body></html>

Tutorial/05 BibTeX in Python/out_2.html

@@ -0,0 +1,28 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN">
+<html>
+<head><meta name="generator" content="Pybtex">
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Bibliography</title>
+</head>
+<body>
+<dl>
+<dt>1</dt>
+<dd><div><h4>Combined Measurement of the Higgs Boson Mass in p p Collisions at s= 7 and 8 TeV with the ATLAS and CMS Experiments</h4><i>Aad, Georges and Abbott, B and Abdallah, J and Abdinov, O and Aben, R and Abolins, M and AbouZeid, OS and Abramowicz, H and Abreu, H and Abreu, R and others</i>
+Physical review letters&nbsp;114&nbsp;(19):191803</div></dd>
+<dt>2</dt>
+<dd><div><h4>The generalized unicorn problem in Finsler geometry</h4><i>Cheng, Xinyue and Zou, Yangyang</i>
+Differential Geometry-Dynamical Systems&nbsp;17:38–48</div></dd>
+<dt>3</dt>
+<dd><div><h4>Unicorn: A system for searching the social graph</h4><i>Curtiss, Michael and Becker, Iain and Bosman, Tudor and Doroshenko, Sergey and Grijincu, Lucian and Jackson, Tom and Kunnatur, Sandhya and Lassen, Soren and Pronin, Philip and Sankar, Sriram and others</i>
+Proceedings of the VLDB Endowment&nbsp;6&nbsp;(11):1150–1161
+<a href="https://doi.org/10.14778/2536222.2536239">[ Publishers's page ]</a></div></dd>
+<dt>4</dt>
+<dd><div><h4>It's a small world</h4><i>Collins, James J and Chow, Carson C</i>
+Nature&nbsp;393&nbsp;(6684):409–410</div></dd>
+<dt>5</dt>
+<dd><div><h4>11 The Death of the Author</h4><i>Barthes, Roland</i>
+Media Texts, Authors and Readers: A Reader:166</div></dd>
+<dt>6</dt>
+<dd><div><h4>The unicorn, the normal curve, and other improbable creatures.</h4><i>Micceri, Theodore</i>
+Psychological bulletin&nbsp;105&nbsp;(1):156</div></dd>
+</dl></body></html>