if reduce(operator.or_,
[x in chunk.lower() for x in useless_lines]): continue
if len(chunk) < 2: continue
outfile.write('%010d|%s\n' % (chunkid, chunk))
chunkmap[fakename].append(chunkid)
chunkid += 1
outfile.close()
print "Saving chunkmap"
pickle.dump(chunkmap, open(outmapname, "wb"), pickle.HIGHEST_PROTOCOL)
print "These files couldn't be processed:"
print '\n'.join(skipped)
print "Opening (or creating) cache in", sys.argv[2]
the_cache=StringDBDict(os.path.join(sys.argv[2], DEFAULT_CACHE_NAME),
file_mode='c')
PubMed.download_many([str(x) for x in known_articles if str(x) not in
the_cache.keys()], download_callback,
parser=Medline.RecordParser())
mti_filename=sys.argv[1]+'.mti'
print "Finished processing the cache. Using the cache to build", \
mti_filename
mti_file=open(mti_filename, "w")
chunkmap={}
hexfinder=re.compile(r'\\x[a-f0-9][a-f0-9]', re.IGNORECASE)
for article in known_articles:
try:
article_record=the_cache[str(article)]
except KeyError:
print "Article doesn't exist in cache. Skipping."
continue
if article_record.abstract=='':
print "Article", article, "has no abstract. Skipping."
class Tree(object):
"""Describes a tree of MeSH terms. The contents should be tree_node,
generated by the build_mesh_tree_file script. The tree contains a
term name (string)->tree_node mapping."""
def __init__(self, filename="*&$#$%#", file_mode="r", cachesize=1048576):
# If the filename isn't specified, use the default one (None has a
# special meaning, so we can't use it - it means create a temp file)
if filename == "*&$#$%#":
filename = _DEFAULT_TREE_DATA
logging.info("Initializing tree with data from %r", filename)
self._tree = StringDBDict(persistent_file=filename,
file_mode=file_mode,
cachesize=cachesize)
self._invlookup = None # Init the inverse name lookup database lazily
self._origname = filename
self.terms = self._tree.keys()
self.terms.sort()
# This one is for speedy retrieval and indexing
self._term_list_as_dict = None
self._search_dict = None
self.num_terms = len(self.terms)
return
def original_filename(self):
"""Returns the original filename of the tree."""
return self._origname
def __repr__(self):
return "<MeSH Semantic tree from %s with %d terms>" % \
(self._origname, self.num_terms)
@staticmethod
def common_root(pos1, pos2):
"""Determines the common dotted root of a pair of tree positions."""
pos1_split = pos1.split(".")
pos2_split = pos2.split(".")
common_terms = []
for x in zip(pos1_split, pos2_split):
if x[0] != x[1]: break
common_terms.append(x[0])
return '.'.join(common_terms)
def semantic_distance(self, term1, term2):
"""Distance between two nodes, assuming there is a single root node
for the tree linking all subtrees. Qualifiers and descriptors are
automatically excluded"""
node1 = self._tree[term1]
node2 = self._tree[term2]
if node1.is_qualifier() or node2.is_qualifier():
return -1
if node1.is_descriptor() or node2.is_descriptor():
return -1
distance = 999999999999
for pos1 in node1.position:
pos1 = '#.%s' % pos1
for pos2 in node2.position:
# The extra item in pos 1 and pos 2 emulates the common root
# node
pos2 = '#.%s' % pos2
root = self.common_root(pos1, pos2)
rootdots = root.count(".")
dist_1 = pos1.count(".") - rootdots
dist_2 = pos2.count(".") - rootdots
dist = dist_1 + dist_2
if dist < 0.0:
raise ValueError(
"Problem: %s<->%s have a negative "
"distance", pos1, pos2)
if dist < distance: distance = dist
return distance
def distance(self, term1, term2):
"""Distance between two nodes, assuming no single root node
for the tree linking all subtrees."""
# Check for same-treeness
possible_trees1 = self._tree[term1].get_trees()
possible_trees2 = self._tree[term2].get_trees()
combination_thereof = [x in possible_trees2 for x in possible_trees1]
if True not in combination_thereof:
return -1
sd = self.semantic_distance(term1, term2)
return sd
def deepest_of_list(self, list_of_terms):
return max(
(self._tree[x].deepest_depth(), x) for x in list_of_terms)[1]
def _init_inverse_lookup(self):
"""Sets up the internal data store to perform reverse lookups."""
logging.debug("First request of a reverse lookup. Building the " \
"inverse lookup dictionary.")
self._invlookup = {}
for k, items in self._tree.iteritems():
for item in items.position:
self._invlookup[item] = k
logging.log(ULTRADEBUG, "Done building inverse lookup dictionary.")
return
def reverse_lookup(self, term):
"""Perform a reverse lookup, after setting up the reverse lookup
dictionary if necessary."""
if self._invlookup is None:
self._init_inverse_lookup()
try:
return self._invlookup[term]
except KeyError:
raise PositionNotInTree("%s is not a position in this tree." %
term)
def __getitem__(self, key):
try:
return self._tree[key.lower()]
except KeyError:
raise TermNotInTree("The term %s is not in the tree %r." %
(key, self))
def eliminate_checktags(self, list_of_terms):
"""Returns a list of terms with the checktags omitted."""
return [x for x in list_of_terms if x not in checktags]
def eliminate_descriptors(self, list_of_terms):
return [x for x in list_of_terms if not self._tree[x].is_descriptor(x)]
def eliminate_qualifiers(self, list_of_terms):
return [x for x in list_of_terms if not self[x].is_qualifier()]
def only_checktags(self, list_of_terms):
return [x for x in list_of_terms if x in checktags]
def only_qualifiers(self, list_of_terms):
return [x for x in list_of_terms if self._tree[x].is_qualifier()]
def only_descriptors(self, list_of_terms):
return [x for x in list_of_terms if self._tree[x].is_descriptor()]
def index(self, term):
"""Returns the index of a term in the sorted term list"""
if self._term_list_as_dict is None:
# Precompute all indexes
logging.debug("Building MeSH tree index.")
currindex = 0
self._term_list_as_dict = {}
for each_term in self.terms:
self._term_list_as_dict[each_term] = currindex
for each_synonym in self[each_term].synonyms:
self._term_list_as_dict[each_synonym] = currindex
currindex += 1
try:
return self._term_list_as_dict[term]
except KeyError:
raise TermNotInTree("Term %s is not a member of tree %r" %
(term, self))
def term_vector(self, list_of_terms):
"""Returns a VocabularyVector representing the list of terms as seen
by this tree."""
new_vector = VocabularyVector(self.num_terms)
for term in list_of_terms:
try:
new_vector[self.index(term)] = 1
except TermNotInTree:
logging.warn(
'Weird: term %r could not be found in %r. It '
'should be there.', term, self)
return new_vector
def _init_search_dict(self):
"""Sets up the internal data store to perform searches."""
logging.debug("First request of a search. Building the " \
"search dictionary.")
self._search_dict = {}
for k, items in self._tree.iteritems():
for synonym in items.synonyms:
if synonym in self._search_dict:
self._search_dict[synonym].append(k)
else:
self._search_dict[synonym] = [k]
if k in self._search_dict:
self._search_dict[k].append(k)
else:
self._search_dict[k] = [k]
def search(self, term):
"""Searches the tree for a term, looking at synonyms as well as keys"""
if self._search_dict is None:
self._init_search_dict()
try:
result = self._search_dict[term]
except KeyError:
return TreeSearchResults([])
if len(result) == 1:
return TreeSearchResults(self[result[0]])
return TreeSearchResults([self[x] for x in result])
class Tree(object):
"""Describes a tree of MeSH terms. The contents should be tree_node,
generated by the build_mesh_tree_file script. The tree contains a
term name (string)->tree_node mapping."""
def __init__(self, filename="*&$#$%#", file_mode="r", cachesize=1048576):
# If the filename isn't specified, use the default one (None has a
# special meaning, so we can't use it - it means create a temp file)
if filename=="*&$#$%#":
filename=_DEFAULT_TREE_DATA
logging.info("Initializing tree with data from %r", filename)
self._tree=StringDBDict(persistent_file=filename, file_mode=file_mode,
cachesize=cachesize)
self._invlookup=None # Init the inverse name lookup database lazily
self._origname=filename
self.terms=self._tree.keys()
self.terms.sort()
# This one is for speedy retrieval and indexing
self._term_list_as_dict=None
self._search_dict=None
self.num_terms=len(self.terms)
return
def original_filename(self):
"""Returns the original filename of the tree."""
return self._origname
def __repr__(self):
return "<MeSH Semantic tree from %s with %d terms>" % \
(self._origname, self.num_terms)
@staticmethod
def common_root(pos1, pos2):
"""Determines the common dotted root of a pair of tree positions."""
pos1_split=pos1.split(".")
pos2_split=pos2.split(".")
common_terms=[]
for x in zip(pos1_split, pos2_split):
if x[0]!=x[1]: break
common_terms.append(x[0])
return '.'.join(common_terms)
def semantic_distance(self, term1, term2):
"""Distance between two nodes, assuming there is a single root node
for the tree linking all subtrees. Qualifiers and descriptors are
automatically excluded"""
node1=self._tree[term1]
node2=self._tree[term2]
if node1.is_qualifier() or node2.is_qualifier():
return -1
if node1.is_descriptor() or node2.is_descriptor():
return -1
distance=999999999999
for pos1 in node1.position:
pos1='#.%s' % pos1
for pos2 in node2.position:
# The extra item in pos 1 and pos 2 emulates the common root
# node
pos2='#.%s' % pos2
root=self.common_root(pos1, pos2)
rootdots=root.count(".")
dist_1=pos1.count(".")-rootdots
dist_2=pos2.count(".")-rootdots
dist=dist_1+dist_2
if dist < 0.0:
raise ValueError("Problem: %s<->%s have a negative "
"distance", pos1, pos2)
if dist < distance: distance=dist
return distance
def distance(self, term1, term2):
"""Distance between two nodes, assuming no single root node
for the tree linking all subtrees."""
# Check for same-treeness
possible_trees1=self._tree[term1].get_trees()
possible_trees2=self._tree[term2].get_trees()
combination_thereof=[x in possible_trees2 for x in possible_trees1]
if True not in combination_thereof:
return -1
sd=self.semantic_distance(term1, term2)
return sd
def deepest_of_list(self, list_of_terms):
return max((self._tree[x].deepest_depth(), x)
for x in list_of_terms)[1]
def _init_inverse_lookup(self):
"""Sets up the internal data store to perform reverse lookups."""
logging.debug("First request of a reverse lookup. Building the " \
"inverse lookup dictionary.")
self._invlookup={}
for k, items in self._tree.iteritems():
for item in items.position:
self._invlookup[item]=k
logging.log(ULTRADEBUG, "Done building inverse lookup dictionary.")
return
def reverse_lookup(self, term):
"""Perform a reverse lookup, after setting up the reverse lookup
dictionary if necessary."""
if self._invlookup is None:
self._init_inverse_lookup()
try:
return self._invlookup[term]
except KeyError:
raise PositionNotInTree("%s is not a position in this tree." %
term)
def __getitem__(self, key):
try:
return self._tree[key.lower()]
except KeyError:
raise TermNotInTree("The term %s is not in the tree %r." %
(key, self))
def eliminate_checktags(self, list_of_terms):
"""Returns a list of terms with the checktags omitted."""
return [x for x in list_of_terms if x not in checktags]
def eliminate_descriptors(self, list_of_terms):
return [x for x in list_of_terms
if not self._tree[x].is_descriptor(x)]
def eliminate_qualifiers(self, list_of_terms):
return [x for x in list_of_terms
if not self[x].is_qualifier()]
def only_checktags(self, list_of_terms):
return [x for x in list_of_terms if x in checktags]
def only_qualifiers(self, list_of_terms):
return [x for x in list_of_terms if self._tree[x].is_qualifier()]
def only_descriptors(self, list_of_terms):
return [x for x in list_of_terms if self._tree[x].is_descriptor()]
def index(self, term):
"""Returns the index of a term in the sorted term list"""
if self._term_list_as_dict is None:
# Precompute all indexes
logging.debug("Building MeSH tree index.")
currindex=0
self._term_list_as_dict={}
for each_term in self.terms:
self._term_list_as_dict[each_term]=currindex
for each_synonym in self[each_term].synonyms:
self._term_list_as_dict[each_synonym]=currindex
currindex+=1
try:
return self._term_list_as_dict[term]
except KeyError:
raise TermNotInTree("Term %s is not a member of tree %r" %
(term, self))
def term_vector(self, list_of_terms):
"""Returns a VocabularyVector representing the list of terms as seen
by this tree."""
new_vector=VocabularyVector(self.num_terms)
for term in list_of_terms:
try:
new_vector[self.index(term)]=1
except TermNotInTree:
logging.warn('Weird: term %r could not be found in %r. It '
'should be there.',
term, self)
return new_vector
def _init_search_dict(self):
"""Sets up the internal data store to perform searches."""
logging.debug("First request of a search. Building the " \
"search dictionary.")
self._search_dict={}
for k, items in self._tree.iteritems():
for synonym in items.synonyms:
if synonym in self._search_dict:
self._search_dict[synonym].append(k)
else:
self._search_dict[synonym]=[k]
if k in self._search_dict:
self._search_dict[k].append(k)
else:
self._search_dict[k]=[k]
def search(self, term):
"""Searches the tree for a term, looking at synonyms as well as keys"""
if self._search_dict is None:
self._init_search_dict()
try:
result=self._search_dict[term]
except KeyError:
return TreeSearchResults([])
if len(result)==1:
return TreeSearchResults(self[result[0]])
return TreeSearchResults([self[x] for x in result])