def reload(self):
"""(Re-)loads the database from filesystem."""
parser = configparser.ConfigParser()
try:
with io.open(self.configPath, encoding="UTF-8") as f:
confFile = f.read()
except IOError:
raise DatabaseFormatError(
'Invalid BibTeX VCS directory "{}": '
"Configuration file bibtexvcs.conf not found.".format(self.directory)
)
# workaround because ConfigParser does not support sectionless entries
try:
parser.read_string("[root]\n" + confFile)
except configparser.Error as e:
raise DatabaseFormatError("Could not parse configuration file '{}':\n\n{}".format(BTVCSCONF, e))
config = parser["root"]
self.bibfileName = config.get("bibfile", "references.bib")
self.journalsName = config.get("journals", "journals.txt")
for path in self.bibfilePath, self.journalsPath:
if not exists(path):
open(path, "a").close()
self.vcs.add(relpath(path, self.directory))
self.bibfile = BibFile(join(self.directory, self.bibfileName))
self.journals = JournalsFile(join(self.directory, self.journalsName))
self.name = config.get("name", "Untitled Bibtex Database")
self.documents = config.get("documents", "Documents")
self.makeJournalBibfiles() # ensure these are up-to-date
self.publicLink = config.get("publicLink", None)
if not exists(self.documentsPath):
os.mkdir(self.documentsPath)
class Database:
"""Represents a complete literature database.
:param directory: Base path of the database.
:type directory: str
The database configuration is read from the file `bbibtexvcs.conf` and from the layout of the
directory that file resides in.
.. attribute:: directory
Absolute path of the root directory of the literature database.
.. attribute:: bibfileName
Name of the main bibtex database file.
.. attribute:: bibfile
:class:`BibFile` object parsed from the bibtex file.
.. attribute:: journalsName
Name of the journals file.
.. attribute:: journals
:class:`JournalsFile` object read from the journals file.
.. attribute:: name
Name of the database.
.. attribute:: documents
Name of the documents directory (relative to :attr:`directory`).
.. attribute:: vcsType
Type of the used VCS system. One of: ``"git"``, ``"mercurial"``, or ``None``
"""
def __init__(self, directory):
self.directory = directory
if exists(join(self.directory, '.git')):
self.vcsType = 'git'
elif exists(join(self.directory, '.hg')):
self.vcsType = 'mercurial'
else:
self.vcsType = None
self._vcs = None
self.reload()
def reload(self):
"""(Re-)loads the database from filesystem."""
parser = configparser.ConfigParser()
try:
with io.open(self.configPath, encoding='UTF-8') as f:
confFile = f.read()
except IOError:
raise DatabaseFormatError('Not a valid BibTeX VCS directory: '
'Configuration file bibtexvcs.conf not found.')
# workaround because ConfigParser does not support sectionless entries
try:
parser.read_string("[root]\n" + confFile)
except configparser.Error as e:
raise DatabaseFormatError("Could not parse configuration file '{}':\n\n{}"
.format(BTVCSCONF, e))
config = parser['root']
self.bibfileName = config.get('bibfile', 'references.bib')
self.journalsName = config.get('journals', 'journals.txt')
for path in self.bibfilePath, self.journalsPath:
if not exists(path):
open(path, 'a').close()
self.vcs.add(relpath(path, self.directory))
self.bibfile = BibFile(join(self.directory, self.bibfileName))
self.journals = JournalsFile(join(self.directory, self.journalsName))
self.name = config.get('name', "Untitled Bibtex Database")
self.documents = config.get('documents', 'Documents')
self.makeJournalBibfiles() # ensure these are up-to-date
self.publicLink = config.get('publicLink', None)
if not exists(self.documentsPath):
os.mkdir(self.documentsPath)
@property
def journalsPath(self):
"""The absolute path of the `journals` file."""
return join(self.directory, self.journalsName)
@property
def documentsPath(self):
"""Absolute path of the `documents` directory."""
return join(self.directory, self.documents)
@property
def bibfilePath(self):
"""Absolute path of the bib file."""
return join(self.directory, self.bibfileName)
@property
def configPath(self):
"""Absolute path of the conf file."""
return join(self.directory, BTVCSCONF)
@property
def checksPath(self):
"""Absolute path of the (optional) checks file."""
return join(self.directory, 'checks.py')
def referencedDocuments(self):
"""Returns a list of all filenames of documents referenced to in the bib file."""
docs = []
for entry in self.bibfile.values():
fname = entry.filename()
if fname:
docs.append(fname)
return docs
def existingDocuments(self):
"""Walks recursively through the :attr:`documents` directory and return the paths of all
files contained in there, relative to :attr:`documentsPath`.
"""
for dirpath, _, filenames in os.walk(self.documentsPath):
for file in filenames:
if file != '.DS_Store':
yield relpath(join(dirpath, file), self.documentsPath)
def strval(self, value):
"""Returns a string value for *value*. If *value* is a :class:`MacroReference`, substitutes
the value (if known).
"""
if isinstance(value, MacroReference):
if value.name in self.bibfile.macroDefinitions:
return self.bibfile.macroDefinitions[value.name]
if value.name in self.journals:
return self.journals[value.name].full
return str(value)
def makeJournalBibfiles(self):
"""Creates or updates the files containing journal macro definitions in full and
abbreviated form, respectively.
"""
base = self.bibfilePath[:-4]
if not exists(base + '_abbr.bib') or not exists(base + '_full.bib') or \
os.path.getmtime(self.journalsPath) > os.path.getmtime(base + '_abbr.bib'):
self.journals.writeBibfiles(base)
def runJabref(self):
"""Tries to open this database's ``.bib`` file with `JabRef`_. Will do the following:
- If there is a file named ``jabref.jar`` in :attr:`directory`, it is run with the
java interpreter through ``java -jar jabref.jar``. If additionally there is a file
``jabref.prefs``, JabRef`s options are imported from that file.
- Otherwise, the command ``jabref`` is executed. To that end, the ``jabref`` binary must
be in the system's ``PATH``.
:returns: The :class:`subprocess.Popen` object corresponding to JabRef process.
"""
shell = False
if exists(join(self.directory, 'jabref.jar')):
if os.name == 'nt':
cmdline = ['start', 'jabref.jar']
shell = True
else:
cmdline = ['java', '-jar', 'jabref.jar']
else:
cmdline = ['jabref']
if exists(join(self.directory, 'jabref.prefs')):
cmdline += ['--primp', join('jabref.prefs')]
else:
cmdline += ['--primp', resource_filename(__name__, 'defaultJabref.prefs')]
cmdline.append(os.curdir + os.sep + self.bibfileName)
try:
return subprocess.Popen(cmdline, shell=shell, cwd=self.directory)
except FileNotFoundError as fnf:
if cmdline[0] in ('java', 'start'):
fnf.strerror = 'Please install Java from http://java.com.'
elif cmdline[0] == 'jabref':
fnf.strerror = 'Please install JabRef from http://jabref.sf.net.'
raise fnf
@property
def vcs(self):
"""The :class:`VCSInterface` object associated to this db.
Will be created on first access.
"""
if self._vcs is None:
self._vcs = VCSInterface.get(self)
return self._vcs
def export(self, templateString=None, docDir=None):
"""Exports the BibTeX database to a string by using the jinja template engine."""
import datetime, hashlib
try:
import jinja2
except ImportError:
raise ImportError('You need to install the jinja2 package in order to export.')
if docDir is None:
docDir = self.documentsPath
def md5filter(value):
return hashlib.md5(value.encode()).hexdigest()
env = jinja2.Environment(autoescape=False)
env.filters['md5'] = md5filter
if templateString is None:
templateString = resource_string(__name__, 'defaultTemplate.html').decode('UTF-8')
template = env.from_string(templateString)
revision = self.vcs.revision()
import locale
locale.setlocale(locale.LC_ALL, '')
now = datetime.datetime.now().strftime('%c')
version = get_distribution('bibtexvcs').version
return template.render(database=self, docDir=docDir, version=version, revision=revision, now=now)
class Database:
"""Represents a complete literature database.
The database configuration is read from the file `bbibtexvcs.conf` and from the layout of the
directory that file resides in.
Parameters
----------
directory : str
Base path of the database.
Attributes
----------
directory : str
Absolute path of the root directory of the literature database.
bibfileName : str
Name of the main bibtex database file.
bibfile : :class:`BibFile`
:class:`BibFile` object parsed from the bibtex file.
journalsName : str
Name of the journals file.
journals : :class:`JournalsFile`
:class:`JournalsFile` object read from the journals file.
name : str
Name of the database.
documents : str
Name of the documents directory (relative to :attr:`directory`).
vcsType : ("git", "mercurial", "local")
Type of the used VCS system.
"""
def __init__(self, directory, vcs=None):
self.directory = directory
if exists(join(self.directory, ".git")):
self.vcsType = "git"
elif exists(join(self.directory, ".hg")):
self.vcsType = "mercurial"
else:
self.vcsType = "local"
self._vcs = vcs
self.reload()
def reload(self):
"""(Re-)loads the database from filesystem."""
parser = configparser.ConfigParser()
try:
with io.open(self.configPath, encoding="UTF-8") as f:
confFile = f.read()
except IOError:
raise DatabaseFormatError(
'Invalid BibTeX VCS directory "{}": '
"Configuration file bibtexvcs.conf not found.".format(self.directory)
)
# workaround because ConfigParser does not support sectionless entries
try:
parser.read_string("[root]\n" + confFile)
except configparser.Error as e:
raise DatabaseFormatError("Could not parse configuration file '{}':\n\n{}".format(BTVCSCONF, e))
config = parser["root"]
self.bibfileName = config.get("bibfile", "references.bib")
self.journalsName = config.get("journals", "journals.txt")
for path in self.bibfilePath, self.journalsPath:
if not exists(path):
open(path, "a").close()
self.vcs.add(relpath(path, self.directory))
self.bibfile = BibFile(join(self.directory, self.bibfileName))
self.journals = JournalsFile(join(self.directory, self.journalsName))
self.name = config.get("name", "Untitled Bibtex Database")
self.documents = config.get("documents", "Documents")
self.makeJournalBibfiles() # ensure these are up-to-date
self.publicLink = config.get("publicLink", None)
if not exists(self.documentsPath):
os.mkdir(self.documentsPath)
def setDefault(self):
"""Set this database as default in config."""
from bibtexvcs import config
config.setDefaultDatabase(self)
@classmethod
def getDefault(cls):
from bibtexvcs import config
directory = config.getDefaultDirectory()
if directory is None:
raise NoDefaultDatabaseError("No default database configured")
return cls(directory)
@property
def journalsPath(self):
"""The absolute path of the `journals` file."""
return join(self.directory, self.journalsName)
@property
def documentsPath(self):
"""Absolute path of the `documents` directory."""
return join(self.directory, self.documents)
@property
def bibfilePath(self):
"""Absolute path of the bib file."""
return join(self.directory, self.bibfileName)
@property
def configPath(self):
"""Absolute path of the conf file."""
return join(self.directory, BTVCSCONF)
@property
def checksPath(self):
"""Absolute path of the (optional) checks file."""
return join(self.directory, "checks.py")
def referencedDocuments(self):
"""Returns a list of all filenames of documents referenced to in the bib file."""
docs = []
for entry in self.bibfile.values():
fname = entry.filename()
if fname:
docs.append(fname)
return docs
def existingDocuments(self):
"""Walks recursively through the :attr:`documents` directory and return the paths of all
files contained in there, relative to :attr:`documentsPath`.
"""
for dirpath, _, filenames in os.walk(self.documentsPath):
for file in filenames:
if file != ".DS_Store":
yield relpath(join(dirpath, file), self.documentsPath)
def strval(self, value):
"""Returns a string value for *value*. If *value* is a :class:`MacroReference`, substitutes
the value (if known).
"""
if isinstance(value, MacroReference):
if value.name in self.bibfile.macroDefinitions:
return self.bibfile.macroDefinitions[value.name]
if value.name in self.journals:
return self.journals[value.name].full
return str(value)
@property
def abbrJournalsName(self):
"""Name of the abbreviated journals string file."""
return self.bibfileName[:-4] + "_abbr.bib"
@property
def fullJournalsName(self):
"""Name of the full journals string file."""
return self.bibfileName[:-4] + "_full.bib"
def makeJournalBibfiles(self):
"""Creates or updates the files containing journal macro definitions in full and
abbreviated form, respectively.
"""
abbr, full = [join(self.directory, name) for name in (self.abbrJournalsName, self.fullJournalsName)]
if not exists(full) or not exists(abbr) or os.path.getmtime(self.journalsPath) > os.path.getmtime(abbr):
self.journals.writeBibfiles(self.bibfilePath[:-4])
def runJabref(self):
"""Tries to open this database's ``.bib`` file with `JabRef`_. Will do the following:
- If there is a file named ``jabref.jar`` in :attr:`directory`, it is run with the
java interpreter through ``java -jar jabref.jar``. If additionally there is a file
``jabref.prefs``, JabRef`s options are imported from that file.
- Otherwise, the command ``jabref`` is executed. To that end, the ``jabref`` binary must
be in the system's ``PATH``.
:returns: The :class:`subprocess.Popen` object corresponding to JabRef process.
"""
shell = False
if exists(join(self.directory, "jabref.jar")):
if os.name == "nt":
cmdline = ["start", "jabref.jar"]
shell = True
else:
cmdline = ["java", "-jar", "jabref.jar"]
else:
cmdline = ["jabref"]
if exists(join(self.directory, "jabref.prefs")):
cmdline += ["--primp", join("jabref.prefs")]
else:
cmdline += ["--primp", resource_filename(__name__, "defaultJabref.prefs")]
cmdline.append(os.curdir + os.sep + self.bibfileName)
try:
return subprocess.Popen(cmdline, shell=shell, cwd=self.directory)
except FileNotFoundError as fnf:
if cmdline[0] in ("java", "start"):
fnf.strerror = "Please install Java from http://java.com."
elif cmdline[0] == "jabref":
fnf.strerror = "Please install JabRef from http://jabref.sf.net."
raise fnf
@property
def vcs(self):
"""The :class:`VCSInterface` object associated to this db.
Will be created on first access.
"""
if self._vcs is None:
self._vcs = VCSInterface.get(self)
return self._vcs
def export(self, templateString=None, docDir=None):
"""Exports the BibTeX database to a string by using the jinja template engine."""
import datetime, hashlib, bibtexvcs
try:
import jinja2
except ImportError:
raise ImportError("You need to install the jinja2 package in order to export.")
if docDir is None:
docDir = self.documentsPath
def md5filter(value):
return hashlib.md5(value.encode()).hexdigest()
env = jinja2.Environment(autoescape=False)
env.filters["md5"] = md5filter
if templateString is None:
templateString = resource_string(__name__, "defaultTemplate.html").decode("UTF-8")
template = env.from_string(templateString)
revision = self.vcs.revision()
import locale
locale.setlocale(locale.LC_ALL, "")
now = datetime.datetime.now().strftime("%c")
version = bibtexvcs.__version__
return template.render(database=self, docDir=docDir, version=version, revision=revision, now=now)
