def editEntry(entry, file_id='both'):
bibtex = backend.getBibtex(entry, file_id)
if bibtex is False:
tools.warning("Entry "+entry+" does not exist.")
return False
if file_id == 'file':
filename = entry
else:
filename = bibtex['file']
new_bibtex = checkBibtex(filename, tools.parsed2Bibtex(bibtex))
# Tag update
if new_bibtex['tag'] != bibtex['tag']:
print("Editing tag, moving file.")
new_name = backend.getNewName(new_bibtex['file'],
new_bibtex,
new_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
new_bibtex['file'] = new_name
try:
shutil.move(bibtex['file'], new_bibtex['file'])
except shutil.Error:
tools.warning('Unable to move file '+bibtex['file']+' to ' +
new_bibtex['file'] + ' according to tag edit.')
try:
if not os.listdir(os.path.dirname(bibtex['file'])):
os.rmdir(os.path.dirname(bibtex['file']))
except OSError:
tools.warning("Unable to delete empty tag dir " +
os.path.dirname(bibtex['file']))
try:
with open(config.get("folder")+'index.bib', 'r', encoding='utf-8') \
as fh:
index = BibTexParser(fh.read())
index = index.get_entry_dict()
except (TypeError, IOError):
tools.warning("Unable to open index file.")
return False
index[new_bibtex['id']] = new_bibtex
backend.bibtexRewrite(index)
return True
def editEntry(entry, file_id='both'):
bibtex = backend.getBibtex(entry, file_id)
if bibtex is False:
tools.warning("Entry " + entry + " does not exist.")
return False
if file_id == 'file':
filename = entry
else:
filename = bibtex['file']
new_bibtex = checkBibtex(filename, tools.parsed2Bibtex(bibtex))
# Tag update
if new_bibtex['tag'] != bibtex['tag']:
print("Editing tag, moving file.")
new_name = backend.getNewName(new_bibtex['file'], new_bibtex,
new_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
new_bibtex['file'] = new_name
try:
shutil.move(bibtex['file'], new_bibtex['file'])
except shutil.Error:
tools.warning('Unable to move file ' + bibtex['file'] + ' to ' +
new_bibtex['file'] + ' according to tag edit.')
try:
if not os.listdir(os.path.dirname(bibtex['file'])):
os.rmdir(os.path.dirname(bibtex['file']))
except OSError:
tools.warning("Unable to delete empty tag dir " +
os.path.dirname(bibtex['file']))
try:
with open(config.get("folder")+'index.bib', 'r', encoding='utf-8') \
as fh:
index = bibtexparser.load(fh)
index = index.entries_dict
except (TypeError, IOError):
tools.warning("Unable to open index file.")
return False
index[new_bibtex['id']] = new_bibtex
backend.bibtexRewrite(index)
return True
def bibtexAppend(data):
"""Append data to the main bibtex file
data is a dict for one entry in bibtex, as the one from bibtexparser output
"""
try:
with open(config.get("folder")+'index.bib', 'a', encoding='utf-8') \
as fh:
fh.write(tools.parsed2Bibtex(data)+"\n")
except IOError as e:
raise e
tools.warning("Unable to open index file.")
return False
def bibtexAppend(data):
"""Append data to the main bibtex file
data is a dict for one entry in bibtex, as the one from bibtexparser output
"""
try:
with open(config.get("folder")+'index.bib', 'a', encoding='utf-8') \
as fh:
fh.write(tools.parsed2Bibtex(data) + "\n")
except IOError as e:
raise e
tools.warning("Unable to open index file.")
return False
def bibtexRewrite(data):
"""Rewrite the bibtex index file.
data is a dict of bibtex entry dict.
"""
bibtex = ''
for entry in data.keys():
bibtex += tools.parsed2Bibtex(data[entry])+"\n"
try:
with open(config.get("folder")+'index.bib', 'w', encoding='utf-8') \
as fh:
fh.write(bibtex)
except (IOError, TypeError):
tools.warning("Unable to open index file.")
return False
def bibtexRewrite(data):
"""Rewrite the bibtex index file.
data is a dict of bibtex entry dict.
"""
bibtex = ''
for entry in data.keys():
bibtex += tools.parsed2Bibtex(data[entry]) + "\n"
try:
with open(config.get("folder")+'index.bib', 'w', encoding='utf-8') \
as fh:
fh.write(bibtex)
except (IOError, TypeError):
tools.warning("Unable to open index file.")
return False
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 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.loads(bib.bibtex())
fetched_bibtex = fetched_bibtex.entries_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 addFile(src, filetype, manual, autoconfirm, tag, rename=True):
"""
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.loads(bibtex)
bibtex = bibtex.entries_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
if rename:
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
try:
shutil.copy2(src, new_name)
except shutil.Error:
new_name = False
sys.exit("Unable to move file to library dir " +
config.get("folder") + ".")
else:
new_name = src
bibtex['file'] = os.path.abspath(new_name)
# 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.loads(bibtex_string)
bibtex = bibtex.entries_dict
try:
bibtex = bibtex[list(bibtex.keys())[0]]
# Check entries are correct
if "title" not in bibtex:
raise AssertionError
if "authors" not in bibtex and "author" not in bibtex:
raise AssertionError
if "year" not in bibtex:
raise AssertionError
# 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):
print("Missing author, year or title in bibtex.")
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.loads(tmpfile.read().decode('utf-8') + "\n")
bibtex = bibtex.entries_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
sys.exit()
elif args.func == 'search':
raise Exception('TODO')
elif args.func == 'open':
for filename in args.ids:
if not openFile(filename):
sys.exit("Unable to open file associated " + "to ident " +
filename)
sys.exit()
elif args.func == 'export':
bibtex = ''
for id in args.ids:
bibtex += tools.parsed2Bibtex(backend.getBibtex(id,
clean=True))
print(bibtex.strip())
sys.exit
elif args.func == 'resync':
confirm = tools.rawInput("Resync files and bibtex index? [y/N] ")
if confirm.lower() == 'y':
resync()
sys.exit()
elif args.func == 'update':
if args.entries is None:
entries = backend.getEntries()
else:
entries = args.entries
for entry in entries:
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
print(paper)
elif args.func == 'search':
raise Exception('TODO')
elif args.func == 'open':
for filename in args.ids:
if not openFile(filename):
sys.exit("Unable to open file associated " +
"to ident "+filename)
sys.exit()
elif args.func == 'export':
bibtex = ''
for id in args.ids:
bibtex += tools.parsed2Bibtex(backend.getBibtex(id,
clean=True))
print(bibtex.strip())
sys.exit
elif args.func == 'resync':
confirm = tools.rawInput("Resync files and bibtex index? [y/N] ")
if confirm.lower() == 'y':
resync()
sys.exit()
elif args.func == 'update':
if args.entries is None:
entries = backend.getEntries()
else:
entries = args.entries
for entry in entries: