Paper class
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Fabien Benureau
parent
d1a4dd584f
commit
161be4f994
308
papers/paper.py
308
papers/paper.py
@ -1,260 +1,55 @@
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import os
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import copy
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import collections
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import unicodedata
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import re
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from cStringIO import StringIO
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import yaml
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from pybtex.database import Entry, BibliographyData, FieldDict, Person
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import files
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DEFAULT_TYPE = 'article'
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CONTROL_CHARS = ''.join(map(unichr, range(0, 32) + range(127, 160)))
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CITEKEY_FORBIDDEN_CHARS = '@\'\\,#}{~%/' # '/' is OK for bibtex but forbidden
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# here since we transform citekeys into filenames
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CITEKEY_EXCLUDE_RE = re.compile('[%s]'
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% re.escape(CONTROL_CHARS + CITEKEY_FORBIDDEN_CHARS))
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BASE_META = {
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'external-document': None,
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'tags': set(),
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'notes': [],
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}
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def str2citekey(s):
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key = unicodedata.normalize('NFKD', unicode(s)).encode('ascii', 'ignore')
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key = CITEKEY_EXCLUDE_RE.sub('', key)
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# Normalize chars and remove non-ascii
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return key
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def get_bibentry_from_file(bibfile):
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"""Extract first entry (supposed to be the only one) from given file.
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"""
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bib_data = files.load_externalbibfile(bibfile)
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first_key = list(bib_data.entries.keys())[0]
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first_entry = bib_data.entries[first_key]
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return first_key, first_entry
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def get_bibentry_from_string(content):
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"""Extract first entry (supposed to be the only one) from given file.
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"""
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bib_data = files.parse_bibdata(StringIO(content))
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first_key = list(bib_data.entries.keys())[0]
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first_entry = bib_data.entries[first_key]
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return first_key, first_entry
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def copy_person(p):
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return Person(first=p.get_part_as_text('first'),
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middle=p.get_part_as_text('middle'),
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prelast=p.get_part_as_text('prelast'),
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last=p.get_part_as_text('last'),
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lineage=p.get_part_as_text('lineage'))
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def copy_bibentry(entry):
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fd = FieldDict(entry.fields.parent, entry.fields)
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persons = dict([(k, [copy_person(p) for p in v])
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for k, v in entry.persons.items()])
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return Entry(entry.type, fields=fd, persons=persons)
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def get_safe_metadata(meta):
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base_meta = Paper.create_meta()
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if meta is not None:
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base_meta.update(meta)
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base_meta['tags'] = set(base_meta['tags'])
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return base_meta
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def get_safe_metadata_from_content(content):
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return get_safe_metadata(yaml.load(content))
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def get_safe_metadata_from_path(metapath):
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if metapath is None:
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content = None
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else:
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content = files.read_yamlfile(metapath)
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return get_safe_metadata(content)
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def check_citekey(citekey):
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# TODO This is not the right way to test that (17/12/2012)
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if unicode(citekey) != str2citekey(citekey):
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raise ValueError("Invalid citekey: %s" % citekey)
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class NoDocumentFile(Exception):
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pass
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from . import bibstruct
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DEFAULT_META = collections.OrderedDict([('docfile', None), ('tags', set()), ('notes', [])])
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DEFAULT_META = {'docfile': None, 'tags': set(), 'notes': []}
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class Paper(object):
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"""Paper class. The object is responsible for the integrity of its own
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data, and for loading and writing it to disc.
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""" Paper class. The object is responsible for the integrity of its data
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The object uses a pybtex.database.BibliographyData object to store
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biblography data and an additional dictionary to store meta data.
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The object is not responsible of any disk i/o.
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self.bibdata is a pybtex.database.BibliographyData object
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self.metadata is a dictionary
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"""
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def __init__(self, bibentry=None, metadata=None, citekey=None):
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if bibentry is None:
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bibentry = Entry(DEFAULT_TYPE)
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self.bibentry = bibentry
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if metadata is None:
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metadata = Paper.create_meta()
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def __init__(self, bibdata, citekey=None, metadata=None):
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self.citekey = citekey
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self.metadata = metadata
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check_citekey(citekey)
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self.citekey = citekey
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self.bibdata = bibdata
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if self.metadata is None:
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self.metadata = copy.deepcopy(DEFAULT_META)
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if self.citekey is None:
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self.citekey = bibstruct.extract_citekey(self.bibdata)
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bibstruct.check_citekey(self.citekey)
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def __eq__(self, other):
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return (isinstance(self, Paper) and type(other) is type(self)
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and self.bibentry == other.bibentry
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and self.bibdata == other.bibdata
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and self.metadata == other.metadata
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and self.citekey == other.citekey)
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and self.citekey == other.citekey)
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def __repr__(self):
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return 'Paper(%s, %s, %s)' % (
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self.citekey, self.bibentry, self.metadata)
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def __str__(self):
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return self.__repr__()
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def deepcopy(self):
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return Paper(citekey =self.citekey,
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metadata=copy.deepcopy(self.metadata),
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bibdata=copy.deepcopy(self.bibdata))
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# TODO add mechanism to verify keys (15/12/2012)
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@property
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def docpath(self):
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return self.metadata.get('docfile', '')
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def get_external_document_path(self):
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if self.metadata['external-document'] is not None:
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return self.metadata['external-document']
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else:
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raise NoDocumentFile
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@docpath.setter
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def docpath(self, path):
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"""Does not verify if the path exists."""
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self.metadata['docfile'] = path
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def get_document_path(self):
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return self.get_external_document_path()
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def set_external_document(self, docpath):
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fullpdfpath = os.path.abspath(docpath)
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files.check_file(fullpdfpath, fail=True)
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self.metadata['external-document'] = fullpdfpath
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def check_document_path(self):
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return files.check_file(self.get_external_document_path())
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def generate_citekey(self):
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"""Generate a citekey from bib_data.
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Raises:
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KeyError if no author nor editor is defined.
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"""
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author_key = 'author'
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if not 'author' in self.bibentry.persons:
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author_key = 'editor'
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try:
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first_author = self.bibentry.persons[author_key][0]
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except KeyError:
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raise ValueError(
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'No author or editor defined: cannot generate a citekey.')
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try:
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year = self.bibentry.fields['year']
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except KeyError:
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year = ''
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citekey = u'{}{}'.format(u''.join(first_author.last()), year)
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return str2citekey(citekey)
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def save(self, bib_filepath, meta_filepath):
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"""Creates a BibliographyData object containing a single entry and
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saves it to disc.
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"""
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if self.citekey is None:
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raise ValueError(
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'No valid citekey initialized. Cannot save paper')
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bibdata = BibliographyData(entries={self.citekey: self.bibentry})
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files.save_bibdata(bibdata, bib_filepath)
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files.save_meta(self.metadata, meta_filepath)
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def update(self, key=None, bib=None, meta=None):
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if key is not None:
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check_citekey(key)
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self.citekey = key
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if bib is not None:
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self.bibentry = bib
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if meta is not None:
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self.metadata = meta
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def get_document_file_from_bibdata(self, remove=False):
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"""Try extracting document file from bib data.
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Raises NoDocumentFile if not found.
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Parameters:
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-----------
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remove: default: False
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remove field after extracting information
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"""
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try:
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field = self.bibentry.fields['file']
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# Check if this is mendeley specific
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for f in field.split(':'):
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if len(f) > 0:
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break
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if remove:
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self.bibentry.fields.pop('file')
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# This is a hck for Mendeley. Make clean
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if f[0] != '/':
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f = '/' + f
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return f
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except (KeyError, IndexError):
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raise NoDocumentFile('No file found in bib data.')
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def copy(self):
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return Paper(bibentry=copy_bibentry(self.bibentry),
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metadata=self.metadata.copy(),
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citekey=self.citekey)
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@classmethod
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def load(cls, bibpath, metapath=None):
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key, entry = get_bibentry_from_file(bibpath)
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metadata = get_safe_metadata_from_path(metapath)
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p = Paper(bibentry=entry, metadata=metadata, citekey=key)
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return p
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@classmethod
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def create_meta(cls):
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return BASE_META.copy()
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@classmethod
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def many_from_path(cls, bibpath):
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"""Extract list of papers found in bibliographic files in path.
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The behavior is to:
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- ignore wrong entries,
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- overwrite duplicated entries.
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:returns: dictionary of (key, paper | exception)
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if loading of entry failed, the excpetion is returned in the
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dictionary in place of the paper
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"""
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bibpath = files.clean_path(bibpath)
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if os.path.isdir(bibpath):
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all_files = [os.path.join(bibpath, f) for f in os.listdir(bibpath)
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if os.path.splitext(f)[-1] in files.BIB_EXTENSIONS]
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else:
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all_files = [bibpath]
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bib_data = [files.load_externalbibfile(f) for f in all_files]
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papers = {}
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for b in bib_data:
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for k in b.entries:
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try:
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papers[k] = Paper(bibentry=b.entries[k], citekey=k)
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except ValueError, e:
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papers[k] = e
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return papers
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# tags
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# tags
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@property
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def tags(self):
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@ -272,42 +67,3 @@ class Paper(object):
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def remove_tag(self, tag):
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"""Remove a tag from a paper if present."""
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self.tags.discard(tag)
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class PaperInRepo(Paper):
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"""Extend paper class with command specific to the case where the paper
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lives in a repository.
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"""
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def __init__(self, repo, *args, **kwargs):
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Paper.__init__(self, *args, **kwargs)
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self.repo = repo
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def get_document_path_in_repo(self):
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return self.repo.find_document(self.citekey)
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def get_document_path(self):
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try:
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return self.get_document_path_in_repo()
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except NoDocumentFile:
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return self.get_external_document_path()
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def copy(self):
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return PaperInRepo.from_paper(self.as_paper().copy(), self.repo)
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def as_paper(self):
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return Paper(bibentry=self.bibentry,
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metadata=self.metadata,
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citekey=self.citekey)
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@classmethod
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def load(cls, repo, bibpath, metapath=None):
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key, entry = get_bibentry_from_file(bibpath)
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metadata = get_safe_metadata_from_path(metapath)
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p = cls(repo, bibentry=entry, metadata=metadata, citekey=key)
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return p
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@classmethod
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def from_paper(cls, paper, repo):
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return cls(repo, bibentry=paper.bibentry, metadata=paper.metadata,
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citekey=paper.citekey)
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