def invoke(self, args, app=None, **kwargs):
from pwkit.io import get_stdout_bytes
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
# Here we have a slight wrinkle from the usual approach. If the argument
# is a DOI, just fetch it without trying to autolearn a database entry.
idtext = args[0]
from .bibcore import classify_pub_ref
kind, content = classify_pub_ref(idtext)
if kind == 'doi':
doi = content
else:
pub = app.locate_or_die(idtext, autolearn=True)
if pub.doi is None:
die('publication "%s" has no associated DOI, which is necessary', idtext)
doi = pub.doi
from .crossref import stream_doi
url, handle = stream_doi(app, doi)
bout = get_stdout_bytes()
for data in handle:
bout.write(data)
def invoke(self, args, app=None, **kwargs):
from .bibtex import get_style_or_die, merge_with_bibtex
if len(args) != 3:
raise multitool.UsageError('expected exactly 3 arguments')
stylename = args[0]
bibfile = args[1]
auxfile = args[2]
style = get_style_or_die(stylename)
# Load cited nicknames
citednicks = set()
for line in io.open(auxfile, 'rt'):
if not line.startswith(r'\citation{'):
continue
line = line.rstrip()
if line[-1] != '}':
warn('unexpected cite line in LaTeX aux file: "%s"', line)
continue
entries = line[10:-1]
# We provide a mechanism for ignoring raw bibtex entries
citednicks.update([e for e in entries.split(',')
if not e.startswith('r.')])
# Ready to write
merge_with_bibtex(app, bibfile, style, citednicks)
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
# Here we have a slight wrinkle from the usual approach. If the argument
# is a bibcode, just fetch it without trying to autolearn a database
# entry.
idtext = args[0]
from .bibcore import classify_pub_ref
kind, content = classify_pub_ref(idtext)
if kind == 'bibcode':
bibcode = content
# XXX: should log a visit if there's a pub, in this case
else:
pub = app.locate_or_die(idtext)
if pub.bibcode is None:
die('cannot open ADS for this publication: no bibcode on record'
)
bibcode = pub.bibcode
app.db.log_action(pub.id, 'visit')
app.open_url('http://labs.adsabs.harvard.edu/adsabs/abs/%s/' %
wu.urlquote(bibcode))
def invoke(self, args, app=None, **kwargs):
if len(args) < 2:
raise multitool.UsageError('expected at least 2 arguments')
groupname = args[0]
# FIXME: check groupname to avoid "bib group add abc+12 xyz+10" mistake
dbgroupname = 'user_' + groupname
# We want to complain if an individual term doesn't match anything in the
# group, but if the user specifies "williams.*" and we get a bunch of hits
# only one of which is in the group, that's OK. So we need to process terms
# individually.
c = app.db.cursor()
try:
for idtext in args[1:]:
ndeleted = 0
for pub in app.locate_pubs((idtext,)):
c.execute('DELETE FROM publists WHERE name == ? AND pubid == ?',
(dbgroupname, pub.id))
ndeleted += c.rowcount
if not ndeleted:
warn('no entries in "%s" matched "%s"', groupname, idtext)
except Exception as e:
die(e)
def invoke(self, args, app=None, **kwargs):
if len(args) not in (0, 1):
raise multitool.UsageError('expected 0 or 1 arguments')
try:
if len(args) == 0:
# List the groups.
q = app.db.execute(
'SELECT DISTINCT name FROM publists WHERE '
'name LIKE ? ORDER BY name ASC', ('user_%', ))
for (name, ) in q:
print(name[5:])
else:
# List the items in a group.
groupname = args[0]
# FIXME: check groupname to avoid "bib group add abc+12 xyz+10" mistake
dbgroupname = 'user_' + groupname
q = app.db.pub_fquery(
'SELECT p.* FROM pubs AS p, publists AS pl '
'WHERE p.id == pl.pubid AND pl.name == ? '
'ORDER BY pl.idx', dbgroupname)
print_generic_listing(app.db, q)
except Exception as e:
die(e)
def invoke(self, args, app=None, **kwargs):
import subprocess
if len(args) < 1:
raise multitool.UsageError('expected at least 1 argument')
for idtext in args:
pub = app.locate_or_die(idtext, autolearn=True)
sha1 = app.db.getfirstval('SELECT sha1 FROM pdfs WHERE pubid = ?', pub.id)
if sha1 is None:
sha1 = app.try_get_pdf(pub)
if sha1 is None:
die('no saved PDF for %s, and cannot figure out how to download it', idtext)
with make_temp_nicename(app.db, pub, sha1) as nicepath:
# TODO: config
subprocess.check_call(
['rmapi', 'put', nicepath, 'Printouts'],
shell = False,
stdout = open(os.devnull, 'wb')
)
# We'll count this as a read
app.db.log_action(pub.id, 'read')
def invoke(self, args, app=None, **kwargs):
if len(args) != 2:
raise multitool.UsageError('expected exactly 2 arguments')
idtext = args[0]
pdfpath = args[1]
import hashlib, shutil
pub = app.locate_or_die(idtext)
# Get SHA1 of the PDF -- we could be more efficient by copying
# to a temporary path while we're at it, but, meh.
with io.open(pdfpath, 'rb') as f:
s = hashlib.sha1()
while True:
b = f.read(4096)
if not len(b):
break
s.update(b)
sha1 = s.hexdigest()
# Copy it into the library
ensure_libpath_exists(sha1)
dest = libpath(sha1, 'pdf')
shutil.copyfile(pdfpath, dest)
# Update the DB
app.db.execute('INSERT OR REPLACE INTO pdfs VALUES (?, ?)', (sha1, pub.id))
def invoke(self, args, app=None, **kwargs):
from . import textfmt
from tempfile import NamedTemporaryFile
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
pub = app.locate_or_die(idtext, autolearn=True)
# While NamedTemporaryFile returns an existing stream, I think we're going
# to have to manually wrap it in a codec.
work = NamedTemporaryFile(prefix='bib.edit.', mode='wb', dir='.', delete=False)
enc = codecs.getwriter('utf-8')(work)
textfmt.export_one(app, pub, enc, 72)
work.close()
run_editor(work.name)
enc = codecs.getreader('utf-8')(open(work.name, 'rb'))
info = textfmt.import_one(enc)
app.db.update_pub(pub, info)
try:
os.unlink(work.name)
except Exception as e:
warn('couldn\'t delete temporary file "%s": %s', work.name, e)
try:
os.unlink(work.name + '~')
except:
pass # whatever.
def invoke(self, args, app=None, **kwargs):
from .db import init
if len(args) != 0:
raise multitool.UsageError('expected no arguments')
init(app)
def invoke(self, args, app=None, tool=None, **kwargs):
if len(args) < 1:
raise multitool.UsageError('expected at least 1 argument')
subcommand = args[0]
from . import completions
completions.process(app, tool, subcommand, args[1:])
def invoke(self, args, app=None, **kwargs):
if len(args) != 0:
raise multitool.UsageError('expected no arguments')
pubs = app.db.pub_fquery(
'SELECT DISTINCT p.* FROM pubs AS p, history AS h '
'WHERE p.id == h.pubid ORDER BY date DESC LIMIT 10')
print_generic_listing(app.db, pubs, sort=None)
def invoke(self, args, app=None, **kwargs):
from .ads import search_ads
# XXX need a real option-parsing setup
rawmode = pop_option('raw', args)
if len(args) < 1:
raise multitool.UsageError('expected arguments')
search_ads(app, parse_search(args), raw=rawmode)
def invoke(self, args, app=None, **kwargs):
from .bibtex import import_stream
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
bibpath = args[0]
with io.open(bibpath, 'rt') as f:
import_stream(app, f)
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
# TODO: should be OK to match multiple publications and print them all
# out.
pub = app.locate_or_die(idtext, autolearn=True)
year = pub.year or 'no year'
title = pub.title or '(no title)'
authors = list(app.db.get_pub_authors(pub.id))
if len(authors) > 10:
authstr = ', '.join(a[1] for a in authors[:10]) + ' ...'
elif len(authors):
authstr = ', '.join(a[1] for a in authors)
else:
authstr = '(no authors)'
bold, bred, red, reset = get_color_codes(None, 'bold', 'bold-red', 'red', 'reset')
print_linewrapped(bred + title + reset, rest_prefix=' ')
print_linewrapped(bold + '%s (%s)' % (authstr, year) + reset, rest_prefix=' ')
nicks = [t[0] for t in app.db.execute('SELECT nickname FROM nicknames '
'WHERE pubid == ? '
'ORDER BY nickname', (pub.id, ))]
if len(nicks):
print(red + 'nicknames:' + reset, *nicks)
if pub.arxiv is not None:
print(red + 'arxiv:' + reset, pub.arxiv)
if pub.bibcode is not None:
print(red + 'bibcode:' + reset, pub.bibcode)
if pub.doi is not None:
print(red + 'DOI:' + reset, pub.doi)
if pub.refdata is not None:
rd = json.loads(pub.refdata)
txt = red + '~BibTeX:' + reset + ' @%s {' % rd.pop('_type')
def fmt(t):
k, v = t
if ' ' in v:
return k + '="' + v + '"'
return k + '=' + v
bits = (fmt(t) for t in sorted(rd.items(), key=lambda t: t[0]))
txt += ', '.join(bits) + '}'
print_linewrapped(txt, rest_prefix=' ')
if pub.abstract is not None:
print()
print_linewrapped(pub.abstract, maxwidth=72)
app.db.log_action(pub.id, 'visit')
def invoke(self, args, app=None, **kwargs):
if len(args) != 0:
raise multitool.UsageError('expected no arguments')
# Note that we've wrapped sys.stdin inside a UTF-8 decoder, so we have to
# check the true underlying stream.
if not sys.stdin.stream.isatty():
die('this command can only be run with standard input set to a TTY')
from .secret import store_user_secret
store_user_secret(app.cfg)
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
# TODO: mode to match multiple publications and delete them
# all, if a --force flag is given.
pub = app.locate_or_die(idtext, autolearn=True)
app.db.delete_pub(pub.id)
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
pub = app.locate_or_die(idtext)
if pub.arxiv is None:
die('cannot open arxiv website: no identifier for record')
app.db.log_action(pub.id, 'visit')
app.open_url('http://arxiv.org/abs/' + wu.urlquote(pub.arxiv))
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
pub = app.locate_or_die(idtext)
if pub.doi is None:
die('cannot open journal website: no DOI for record')
app.db.log_action(pub.id, 'visit')
app.open_url('http://dx.doi.org/' + wu.urlquote(pub.doi))
def invoke(self, args, app=None, **kwargs):
from .bibtex import get_style_or_die, export_to_bibtex
if len(args) < 2:
raise multitool.UsageError('expected at least 2 arguments')
stylename = args[0]
nicks = args[1:]
style = get_style_or_die(stylename)
# That's all there is to it.
export_to_bibtex(app, style, nicks)
def invoke(self, args, app=None, **kwargs):
long_listing = pop_option('l', args)
if len(args) != 0:
raise multitool.UsageError('expected no non-option arguments')
if long_listing:
n = 100
else:
n = 10
pubs = app.db.pub_fquery('SELECT DISTINCT p.* FROM pubs AS p, history AS h '
'WHERE p.id == h.pubid ORDER BY date DESC LIMIT ?', n)
print_generic_listing(app.db, pubs, sort=None)
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
pub = app.locate_or_die(idtext)
sha1 = app.db.getfirstval('SELECT sha1 FROM pdfs WHERE pubid = ?', pub.id)
if sha1 is None:
# XXX: only do this optionally, maybe?
sha1 = app.try_get_pdf(pub)
if sha1 is not None:
print(libpath(sha1, 'pdf'))
def invoke(self, args, app=None, **kwargs):
if len(args) < 2:
raise multitool.UsageError('expected at least 2 arguments')
groupname = args[0]
# FIXME: check groupname to avoid "bib group add abc+12 xyz+10" mistake
dbgroupname = 'user_' + groupname
try:
for pub in app.locate_pubs(args[1:], autolearn=True):
app.db.execute('INSERT OR IGNORE INTO publists VALUES (?, '
' (SELECT ifnull(max(idx)+1,0) FROM publists WHERE name == ?), '
'?)', (dbgroupname, dbgroupname, pub.id))
except Exception as e:
die(e)
def invoke(self, args, app=None, **kwargs):
import re
nocase = pop_option('i', args)
fixed = pop_option('f', args)
refinfo = pop_option('r', args)
if len(args) != 1:
raise multitool.UsageError(
'expected exactly 1 non-option argument')
regex = args[0]
if refinfo:
fields = ['arxiv', 'bibcode', 'doi', 'refdata']
else:
fields = ['title', 'abstract']
try:
# Could use the Sqlite REGEXP machinery, but it should be somewhat
# faster to precompile the regex. Premature optimization FTW.
if fixed:
def rmatch(i):
if i is None:
return False
return regex in i
else:
flags = 0
if nocase:
flags |= re.IGNORECASE
comp = re.compile(regex, flags)
def rmatch(i):
if i is None:
return False
return comp.search(i) is not None
app.db.create_function('rmatch', 1, rmatch)
q = app.db.pub_fquery('SELECT * FROM pubs WHERE ' +
'||'.join('rmatch(%s)' % f for f in fields))
print_generic_listing(app.db, q)
except Exception as e:
die(e)
def invoke(self, args, app=None, **kwargs):
from .bibtex import bibtex_styles, export_to_bibtex
if len(args) < 2:
raise multitool.UsageError('expected at least 2 arguments')
outstyle = args[0]
nicks = args[1:]
# Load/check style
factory = bibtex_styles.get(outstyle)
if factory is None:
die('unrecognized BibTeX output style "%s"', outstyle)
style = factory()
# That's all there is to it.
export_to_bibtex(app, style, nicks)
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
pub = app.locate_or_die(idtext, autolearn=True)
sha1 = app.db.getfirstval('SELECT sha1 FROM pdfs WHERE pubid = ?', pub.id)
if sha1 is None:
sha1 = app.try_get_pdf(pub)
if sha1 is None:
die('no saved PDF for %s, and cannot figure out how to download it', idtext)
app.db.log_action(pub.id, 'read')
pdfreader = app.cfg.get_or_die('apps', 'pdf-reader')
launch_background_silent(pdfreader, [pdfreader, libpath(sha1, 'pdf')])
def invoke(self, args, app=None, **kwargs):
if len(args) not in (2, 3):
raise multitool.UsageError('expected 2 or 3 arguments')
oldjournal = args[0]
newjournal = args[1]
newissn = args[2] if len(args) > 2 else None
for pub in app.db.pub_query('refdata NOT NULL'):
rd = json.loads(pub.refdata)
if rd.get('journal', '') != oldjournal:
continue
rd['journal'] = newjournal
if 'issn' not in rd and newissn is not None:
rd['issn'] = newissn
app.db.execute('UPDATE pubs SET refdata = ? WHERE id == ?',
(json.dumps(rd), pub.id))
def invoke(self, args, app=None, **kwargs):
if len(args) != 1:
raise multitool.UsageError('expected exactly 1 argument')
idtext = args[0]
pub = app.locate_or_die(idtext)
# It's not something I plan to do, but the schema does let us
# store multiple PDFs for one pub ...
any = False
for (sha1, ) in app.db.execute('SELECT sha1 FROM pdfs '
'WHERE pubid == ?', (pub.id, )):
print('orphaning', libpath(sha1, 'pdf'))
any = True
if not any:
warn('no PDFs were on file for "%s"', idtext)
app.db.execute('DELETE FROM pdfs WHERE pubid == ?', (pub.id, ))
def invoke(self, args, app=None, **kwargs):
import re
from .bibtex import get_style_or_die
if len(args) != 2:
raise multitool.UsageError('expected exactly 2 non-option arguments')
stylename = args[0]
regex = args[1].encode('utf8')
style = get_style_or_die(stylename)
comp = re.compile(regex, re.IGNORECASE)
inm = getattr(style, 'issn_name_map', None)
if inm is None:
die('style "%s" does not provide an ISSN/journal-name map', stylename)
# t = (issn, jname):
matches = (t for t in six.viewitems(inm)
if comp.search(t[1]) is not None)
for issn, jname in sorted(matches, key=lambda t: t[0]):
print('%s %s' % (issn, jname.decode('utf8')))
def invoke(self, args, app=None, **kwargs):
from .bibtex import bibtex_styles, export_to_bibtex
if len(args) != 2:
raise multitool.UsageError('expected exactly 2 arguments')
outstyle = args[0]
auxfile = args[1]
# Load/check style
factory = bibtex_styles.get(outstyle)
if factory is None:
die('unrecognized BibTeX output style "%s"', outstyle)
style = factory()
# Load cited nicknames
citednicks = set()
for line in io.open(auxfile, 'rt'):
if not line.startswith(r'\citation{'):
continue
line = line.rstrip()
if line[-1] != '}':
warn('unexpected cite line in LaTeX aux file: "%s"', line)
continue
entries = line[10:-1]
# We provide a mechanism for ignoring raw bibtex entries
citednicks.update(
[e for e in entries.split(',') if not e.startswith('r.')])
# Ready to write
export_to_bibtex(app, style, citednicks)
def invoke(self, args, app=None, **kwargs):
if len(args) != 0:
raise multitool.UsageError('expected no arguments')
app.rsync_backup()
