def updateArXiv(entry):
"""Look for new versions of arXiv entry `entry`
Returns False if no new versions or not an arXiv entry,
Returns the new bibtex otherwise.
"""
bibtex = getBibtex(entry)
# Check arXiv
if('archiveprefix' not in bibtex or
'arXiv' not in bibtex['archiveprefix']):
return False
arxiv_id = bibtex['eprint']
arxiv_id_no_v = re.sub(r'v\d+\Z', '', arxiv_id)
ids = set(arxiv_id)
for entry in getEntries():
if('archiveprefix' not in bibtex or
'arXiv' not in bibtex['archiveprefix']):
continue
ids.add(bibtex['eprint'])
last_bibtex = BibTexParser(fetcher.arXiv2Bib(arxiv_id_no_v))
last_bibtex = last_bibtex.get_entry_dict()
last_bibtex = last_bibtex[list(last_bibtex.keys())[0]]
if last_bibtex['eprint'] not in ids:
return last_bibtex
else:
return False
def getBibtex(entry, file_id='both', clean=False):
"""Returns the bibtex entry corresponding to entry, as a dict
entry is either a filename or a bibtex ident
file_id is file or id or both to search for a file / id / both
clean is to clean the ignored fields specified in config
"""
try:
with open(config.get("folder")+'index.bib', 'r', encoding='utf-8') \
as fh:
bibtex = BibTexParser(fh.read())
bibtex = bibtex.get_entry_dict()
except (TypeError, IOError):
tools.warning("Unable to open index file.")
return False
bibtex_entry = False
if file_id == 'both' or file_id == 'id':
try:
bibtex_entry = bibtex[entry]
except KeyError:
pass
if file_id == 'both' or file_id == 'file':
if os.path.isfile(entry):
for key in bibtex.keys():
if os.path.samefile(bibtex[key]['file'], entry):
bibtex_entry = bibtex[key]
break
if clean:
for field in config.get("ignore_fields"):
try:
del(bibtex_entry[field])
except KeyError:
pass
return bibtex_entry
def deleteId(ident):
"""Delete a file based on its id in the bibtex file"""
try:
with open(config.get("folder")+'index.bib', 'r', encoding='utf-8') \
as fh:
bibtex = BibTexParser(fh.read())
bibtex = bibtex.get_entry_dict()
except (IOError, TypeError):
tools.warning("Unable to open index file.")
return False
if ident not in bibtex.keys():
return False
try:
os.remove(bibtex[ident]['file'])
except (KeyError, OSError):
tools.warning("Unable to delete file associated to id "+ident+" : " +
bibtex[ident]['file'])
try:
if not os.listdir(os.path.dirname(bibtex[ident]['file'])):
os.rmdir(os.path.dirname(bibtex[ident]['file']))
except (KeyError, OSError):
tools.warning("Unable to delete empty tag dir " +
os.path.dirname(bibtex[ident]['file']))
try:
del(bibtex[ident])
bibtexRewrite(bibtex)
except KeyError:
tools.warning("No associated bibtex entry in index for file " +
bibtex[ident]['file'])
return True
def getEntries():
"""Returns the list of all entries in the bibtex index"""
try:
with open(config.get("folder")+'index.bib', 'r', encoding='utf-8') \
as fh:
bibtex = BibTexParser(fh.read())
bibtex = bibtex.get_entry_dict()
except (TypeError, IOError):
tools.warning("Unable to open index file.")
return False
return list(bibtex.keys())
def openFile(ident):
try:
with open(config.get("folder")+'index.bib', 'r', encoding='utf-8') \
as fh:
bibtex = BibTexParser(fh.read())
bibtex = bibtex.get_entry_dict()
except (TypeError, IOError):
tools.warning("Unable to open index file.")
return False
if ident not in list(bibtex.keys()):
return False
else:
subprocess.Popen(['xdg-open', bibtex[ident]['file']])
return True
def arXiv2Bib(arxiv):
"""Returns bibTeX string of metadata for a given arXiv id
arxiv is an arxiv id
"""
bibtex = arxiv_metadata.arxiv2bib([arxiv])
for bib in bibtex:
if isinstance(bib, arxiv_metadata.ReferenceErrorInfo):
continue
else:
fetched_bibtex = BibTexParser(bib.bibtex())
fetched_bibtex = fetched_bibtex.get_entry_dict()
fetched_bibtex = fetched_bibtex[list(fetched_bibtex.keys())[0]]
try:
del(fetched_bibtex['file'])
except KeyError:
pass
return tools.parsed2Bibtex(fetched_bibtex)
return ''
def deleteFile(filename):
"""Delete a file based on its filename"""
try:
with open(config.get("folder")+'index.bib', 'r', encoding='utf-8') \
as fh:
bibtex = BibTexParser(fh.read())
bibtex = bibtex.get_entry_dict()
except (TypeError, IOError):
tools.warning("Unable to open index file.")
return False
found = False
for key in list(bibtex.keys()):
try:
if os.path.samefile(bibtex[key]['file'], filename):
found = True
try:
os.remove(bibtex[key]['file'])
except (KeyError, OSError):
tools.warning("Unable to delete file associated to id " +
key+" : "+bibtex[key]['file'])
try:
if not os.listdir(os.path.dirname(filename)):
os.rmdir(os.path.dirname(filename))
except OSError:
tools.warning("Unable to delete empty tag dir " +
os.path.dirname(filename))
try:
del(bibtex[key])
except KeyError:
tools.warning("No associated bibtex entry in index for " +
"file " + bibtex[key]['file'])
except (KeyError, OSError):
pass
if found:
bibtexRewrite(bibtex)
elif os.path.isfile(filename):
os.remove(filename)
return found
class TestFetcher(unittest.TestCase):
def setUp(self):
config.set("folder", tempfile.mkdtemp()+"/")
self.bibtex_article_string = """
@article{1303.3130v1,
abstract={We study the role of the dipolar interaction, correctly accounting for the
Dipolar-Induced Resonance (DIR), in a quasi-one-dimensional system of ultracold
bosons. We first show how the DIR affects the lowest-energy states of two
particles in a harmonic trap. Then, we consider a deep optical lattice loaded
with ultracold dipolar bosons. We describe this many-body system using an
atom-dimer extended Bose-Hubbard model. We analyze the impact of the DIR on the
phase diagram at T=0 by exact diagonalization of a small-sized system. In
particular, the resonance strongly modifies the range of parameters for which a
mass density wave should occur.},
archiveprefix={arXiv},
author={N. Bartolo and D. J. Papoular and L. Barbiero and C. Menotti and A. Recati},
eprint={1303.3130v1},
file={%sN_Bartolo_A_Recati-j-2013.pdf},
link={http://arxiv.org/abs/1303.3130v1},
month={Mar},
primaryclass={cond-mat.quant-gas},
tag={},
title={Dipolar-Induced Resonance for Ultracold Bosons in a Quasi-1D Optical
Lattice},
year={2013},
}""" % config.get("folder")
self.bibtex_article = BibTexParser(self.bibtex_article_string).get_entry_dict()
self.bibtex_article = self.bibtex_article[list(self.bibtex_article.keys())[0]]
self.bibtex_book_string = """
@book{9780521846516,
author={C. J. Pethick and H. Smith},
isbn={9780521846516},
publisher={Cambridge University Press},
title={Bose-Einstein Condensation In Dilute Gases},
year={2008},
}
"""
self.bibtex_book = BibTexParser(self.bibtex_book_string).get_entry_dict()
self.bibtex_book = self.bibtex_book[list(self.bibtex_book.keys())[0]]
def test_getNewName_article(self):
self.assertEqual(getNewName("test.pdf", self.bibtex_article),
config.get("folder")+"N_Bartolo_A_Recati-j-2013-v1.pdf")
def test_getNewName_article_override(self):
self.assertEqual(getNewName("test.pdf", self.bibtex_article, override_format="%f"),
config.get("folder")+"N_Bartolo.pdf")
def test_getNewName_book(self):
self.assertEqual(getNewName("test.pdf", self.bibtex_book),
config.get("folder")+"C_J_Pethick_H_Smith-Bose-Einstein_Condensation_In_Dilute_Gases.pdf")
def test_getNewName_book_override(self):
self.assertEqual(getNewName("test.pdf", self.bibtex_book, override_format="%a"),
config.get("folder")+"C_J_Pethick_H_Smith.pdf")
def test_bibtexAppend(self):
bibtexAppend(self.bibtex_article)
with open(config.get("folder")+'index.bib', 'r') as fh:
self.assertEqual(fh.read(),
'@article{1303.3130v1,\n\tabstract={We study the role of the dipolar interaction, correctly accounting for the\nDipolar-Induced Resonance (DIR), in a quasi-one-dimensional system of ultracold\nbosons. We first show how the DIR affects the lowest-energy states of two\nparticles in a harmonic trap. Then, we consider a deep optical lattice loaded\nwith ultracold dipolar bosons. We describe this many-body system using an\natom-dimer extended Bose-Hubbard model. We analyze the impact of the DIR on the\nphase diagram at T=0 by exact diagonalization of a small-sized system. In\nparticular, the resonance strongly modifies the range of parameters for which a\nmass density wave should occur.},\n\tarchiveprefix={arXiv},\n\tauthor={N. Bartolo and D. J. Papoular and L. Barbiero and C. Menotti and A. Recati},\n\teprint={1303.3130v1},\n\tfile={'+config.get("folder")+'N_Bartolo_A_Recati-j-2013.pdf},\n\tlink={http://arxiv.org/abs/1303.3130v1},\n\tmonth={Mar},\n\tprimaryclass={cond-mat.quant-gas},\n\ttag={},\n\ttitle={Dipolar-Induced Resonance for Ultracold Bosons in a Quasi-1D Optical\nLattice},\n\tyear={2013},\n}\n\n\n')
def test_bibtexEdit(self):
bibtexAppend(self.bibtex_article)
bibtexEdit(self.bibtex_article['id'], {'id': 'bidule'})
with open(config.get("folder")+'index.bib', 'r') as fh:
self.assertEqual(fh.read(),
'@article{bidule,\n\tabstract={We study the role of the dipolar interaction, correctly accounting for the\nDipolar-Induced Resonance (DIR), in a quasi-one-dimensional system of ultracold\nbosons. We first show how the DIR affects the lowest-energy states of two\nparticles in a harmonic trap. Then, we consider a deep optical lattice loaded\nwith ultracold dipolar bosons. We describe this many-body system using an\natom-dimer extended Bose-Hubbard model. We analyze the impact of the DIR on the\nphase diagram at T=0 by exact diagonalization of a small-sized system. In\nparticular, the resonance strongly modifies the range of parameters for which a\nmass density wave should occur.},\n\tarchiveprefix={arXiv},\n\tauthor={N. Bartolo and D. J. Papoular and L. Barbiero and C. Menotti and A. Recati},\n\teprint={1303.3130v1},\n\tfile={'+config.get("folder")+'N_Bartolo_A_Recati-j-2013.pdf},\n\tlink={http://arxiv.org/abs/1303.3130v1},\n\tmonth={Mar},\n\tprimaryclass={cond-mat.quant-gas},\n\ttag={},\n\ttitle={Dipolar-Induced Resonance for Ultracold Bosons in a Quasi-1D Optical\nLattice},\n\tyear={2013},\n}\n\n\n')
def test_bibtexRewrite(self):
bibtexAppend(self.bibtex_book)
bibtexRewrite({0: self.bibtex_article})
with open(config.get("folder")+'index.bib', 'r') as fh:
self.assertEqual(fh.read(),
'@article{1303.3130v1,\n\tabstract={We study the role of the dipolar interaction, correctly accounting for the\nDipolar-Induced Resonance (DIR), in a quasi-one-dimensional system of ultracold\nbosons. We first show how the DIR affects the lowest-energy states of two\nparticles in a harmonic trap. Then, we consider a deep optical lattice loaded\nwith ultracold dipolar bosons. We describe this many-body system using an\natom-dimer extended Bose-Hubbard model. We analyze the impact of the DIR on the\nphase diagram at T=0 by exact diagonalization of a small-sized system. In\nparticular, the resonance strongly modifies the range of parameters for which a\nmass density wave should occur.},\n\tarchiveprefix={arXiv},\n\tauthor={N. Bartolo and D. J. Papoular and L. Barbiero and C. Menotti and A. Recati},\n\teprint={1303.3130v1},\n\tfile={%sN_Bartolo_A_Recati-j-2013.pdf},\n\tlink={http://arxiv.org/abs/1303.3130v1},\n\tmonth={Mar},\n\tprimaryclass={cond-mat.quant-gas},\n\ttag={},\n\ttitle={Dipolar-Induced Resonance for Ultracold Bosons in a Quasi-1D Optical\nLattice},\n\tyear={2013},\n}\n\n\n' % config.get("folder"))
def test_deleteId(self):
self.bibtex_article['file'] = config.get("folder")+'test.pdf'
bibtexAppend(self.bibtex_article)
open(config.get("folder")+'test.pdf', 'w').close()
deleteId(self.bibtex_article['id'])
with open(config.get("folder")+'index.bib', 'r') as fh:
self.assertEqual(fh.read().strip(), "")
self.assertFalse(os.path.isfile(config.get("folder")+'test.pdf'))
def test_deleteFile(self):
self.bibtex_article['file'] = config.get("folder")+'test.pdf'
bibtexAppend(self.bibtex_article)
open(config.get("folder")+'test.pdf', 'w').close()
deleteFile(self.bibtex_article['file'])
with open(config.get("folder")+'index.bib', 'r') as fh:
self.assertEqual(fh.read().strip(), "")
self.assertFalse(os.path.isfile(config.get("folder")+'test.pdf'))
def test_diffFilesIndex(self):
# TODO
return
def test_getBibtex(self):
bibtexAppend(self.bibtex_article)
got = getBibtex(self.bibtex_article['id'])
self.assertEqual(got, self.bibtex_article)
def test_getBibtex_id(self):
bibtexAppend(self.bibtex_article)
got = getBibtex(self.bibtex_article['id'], file_id='id')
self.assertEqual(got, self.bibtex_article)
def test_getBibtex_file(self):
self.bibtex_article['file'] = config.get("folder")+'test.pdf'
open(config.get("folder")+'test.pdf', 'w').close()
bibtexAppend(self.bibtex_article)
got = getBibtex(self.bibtex_article['file'], file_id='file')
self.assertEqual(got, self.bibtex_article)
def test_getBibtex_clean(self):
config.set("ignore_fields", ['id', 'abstract'])
bibtexAppend(self.bibtex_article)
got = getBibtex(self.bibtex_article['id'], clean=True)
for i in config.get("ignore_fields"):
self.assertNotIn(i, got)
def test_getEntries(self):
bibtexAppend(self.bibtex_article)
self.assertEqual(getEntries(),
[self.bibtex_article['id']])
def test_updateArxiv(self):
# TODO
return
def test_search(self):
# TODO
return
def tearDown(self):
shutil.rmtree(config.get("folder"))
def addFile(src, filetype, manual, autoconfirm, tag):
"""
Add a file to the library
"""
doi = False
arxiv = False
isbn = False
if not manual:
try:
if filetype == 'article' or filetype is None:
id_type, article_id = fetcher.findArticleID(src)
if id_type == "DOI":
doi = article_id
elif id_type == "arXiv":
arxiv = article_id
if filetype == 'book' or (doi is False and arxiv is False and
filetype is None):
isbn = fetcher.findISBN(src)
except KeyboardInterrupt:
doi = False
arxiv = False
isbn = False
if doi is False and isbn is False and arxiv is False:
if filetype is None:
tools.warning("Could not determine the DOI nor the arXiv id nor " +
"the ISBN for "+src+". Switching to manual entry.")
doi_arxiv_isbn = ''
while(doi_arxiv_isbn not in
['doi', 'arxiv', 'isbn', 'manual', 'skip']):
doi_arxiv_isbn = (tools.rawInput("DOI / arXiv " +
"/ ISBN / manual / skip? ").
lower())
if doi_arxiv_isbn == 'doi':
doi = tools.rawInput('DOI? ')
elif doi_arxiv_isbn == 'arxiv':
arxiv = tools.rawInput('arXiv id? ')
elif doi_arxiv_isbn == 'isbn':
isbn = tools.rawInput('ISBN? ')
elif doi_arxiv_isbn == 'skip':
return False
elif filetype == 'article':
tools.warning("Could not determine the DOI nor the arXiv id for " +
src+", switching to manual entry.")
doi_arxiv = ''
while doi_arxiv not in ['doi', 'arxiv', 'manual', 'skip']:
doi_arxiv = (tools.rawInput("DOI / arXiv / manual / skip? ").
lower())
if doi_arxiv == 'doi':
doi = tools.rawInput('DOI? ')
elif doi_arxiv == 'arxiv':
arxiv = tools.rawInput('arXiv id? ')
elif doi_arxiv == 'skip':
return False
elif filetype == 'book':
isbn_manual = ''
while isbn_manual not in ['isbn', 'manual', 'skip']:
isbn_manual = tools.rawInput("ISBN / manual / skip? ").lower()
if isbn_manual == 'isbn':
isbn = (tools.rawInput('ISBN? ').
replace(' ', '').
replace('-', ''))
elif isbn_manual == 'skip':
return False
elif doi is not False:
print("DOI for "+src+" is "+doi+".")
elif arxiv is not False:
print("ArXiv id for "+src+" is "+arxiv+".")
elif isbn is not False:
print("ISBN for "+src+" is "+isbn+".")
if doi is not False and doi != '':
# Add extra \n for bibtexparser
bibtex = fetcher.doi2Bib(doi).strip().replace(',', ",\n")+"\n"
elif arxiv is not False and arxiv != '':
bibtex = fetcher.arXiv2Bib(arxiv).strip().replace(',', ",\n")+"\n"
elif isbn is not False and isbn != '':
# Idem
bibtex = fetcher.isbn2Bib(isbn).strip()+"\n"
else:
bibtex = ''
bibtex = BibTexParser(bibtex)
bibtex = bibtex.get_entry_dict()
if len(bibtex) > 0:
bibtex_name = list(bibtex.keys())[0]
bibtex = bibtex[bibtex_name]
bibtex_string = tools.parsed2Bibtex(bibtex)
else:
bibtex_string = ''
if not autoconfirm:
bibtex = checkBibtex(src, bibtex_string)
if not autoconfirm:
tag = tools.rawInput("Tag for this paper (leave empty for default) ? ")
else:
tag = args.tag
bibtex['tag'] = tag
new_name = backend.getNewName(src, bibtex, tag)
while os.path.exists(new_name):
tools.warning("file "+new_name+" already exists.")
default_rename = new_name.replace(tools.getExtension(new_name),
" (2)"+tools.getExtension(new_name))
rename = tools.rawInput("New name ["+default_rename+"]? ")
if rename == '':
new_name = default_rename
else:
new_name = rename
bibtex['file'] = new_name
try:
shutil.copy2(src, new_name)
except shutil.Error:
new_name = False
sys.exit("Unable to move file to library dir " +
config.get("folder")+".")
# Remove first page of IOP papers
try:
if 'IOP' in bibtex['publisher'] and bibtex['type'] == 'article':
tearpages.tearpage(new_name)
except (KeyError, shutil.Error, IOError):
pass
backend.bibtexAppend(bibtex)
return new_name
def checkBibtex(filename, bibtex_string):
print("The bibtex entry found for "+filename+" is:")
bibtex = BibTexParser(bibtex_string)
bibtex = bibtex.get_entry_dict()
try:
bibtex = bibtex[list(bibtex.keys())[0]]
# Check entries are correct
assert bibtex['title']
if bibtex['type'] == 'article':
assert bibtex['authors']
elif bibtex['type'] == 'book':
assert bibtex['author']
assert bibtex['year']
# Print the bibtex and confirm
print(tools.parsed2Bibtex(bibtex))
check = tools.rawInput("Is it correct? [Y/n] ")
except KeyboardInterrupt:
sys.exit()
except (IndexError, KeyError, AssertionError):
check = 'n'
try:
old_filename = bibtex['file']
except KeyError:
old_filename = False
while check.lower() == 'n':
with tempfile.NamedTemporaryFile(suffix=".tmp") as tmpfile:
tmpfile.write(bibtex_string.encode('utf-8'))
tmpfile.flush()
subprocess.call([EDITOR, tmpfile.name])
tmpfile.seek(0)
bibtex = BibTexParser(tmpfile.read().decode('utf-8')+"\n")
bibtex = bibtex.get_entry_dict()
try:
bibtex = bibtex[list(bibtex.keys())[0]]
except (IndexError, KeyError):
tools.warning("Invalid bibtex entry")
bibtex_string = ''
tools.rawInput("Press Enter to go back to editor.")
continue
if('authors' not in bibtex and 'title' not in bibtex and 'year' not in
bibtex):
tools.warning("Invalid bibtex entry")
bibtex_string = ''
tools.rawInput("Press Enter to go back to editor.")
continue
if old_filename is not False and 'file' not in bibtex:
tools.warning("Invalid bibtex entry. No filename given.")
tools.rawInput("Press Enter to go back to editor.")
check = 'n'
else:
bibtex_string = tools.parsed2Bibtex(bibtex)
print("\nThe bibtex entry for "+filename+" is:")
print(bibtex_string)
check = tools.rawInput("Is it correct? [Y/n] ")
if old_filename is not False and old_filename != bibtex['file']:
try:
print("Moving file to new location…")
shutil.move(old_filename, bibtex['file'])
except shutil.Error:
tools.warning("Unable to move file "+old_filename+" to " +
bibtex['file']+". You should check it manually.")
return bibtex
