def __init__(self, f):
self._artifacts = []
root = ElementTree().parse(f)
for artifact in root.find('artifacts'):
self._artifacts.append(Artifact(artifact))
def dump(self, output):
tempo = {}
root = Element('resources')
root.tail = '\n'
tempo[()] = root
for key in self._resources_order:
for i in range(1, len(key) + 1):
if key[0:i] not in tempo:
parent = tempo[key[0:i - 1]]
value = self._resources.get(key[0:i], None)
if value is None:
elem = SubElement(parent, 'node', name=key[i - 1])
else:
fullKey = key[0]
for j in range(1, i):
fullKey += '/' + key[j]
newValue = self._dictionary[fullKey]
elem = SubElement(parent,
'node',
name=key[i - 1],
value=newValue)
parent.text = elem.tail = '\n' + i * SPACES
tempo[key[0:i]] = elem
fix_it(root)
print >> output, '<?xml version="1.0" encoding="UTF-8"?>'
ElementTree(root).write(output, 'ascii')
def write(pattern, fpath):
import os
from elementtree.ElementTree import Element, ElementTree
root = Element('xml')
toelem(pattern, root)
ElementTree(root).write(fpath)
os.system('tidy -xml -iqm \"%s\"' % fpath)
def __call__ (self) :
self.processed = {}
self.pending = {}
tree = Element ("project", id = "SW-Tasks")
SubElement (tree, "label").text = ("Task(s) %s." % self.toplevel)
SubElement (tree, "import-resources", file = "workers.xml")
if self.VERBOSE > 1 :
self.debug ("Writing `part_of` tree ...")
for issue_id in self.toplevel :
if self.VERBOSE > 2 :
self.debug \
("Issue %d is top-level. Processing it now ..." % issue_id)
issue = self.db.issue.getnode (issue_id)
self.process_issue (issue, tree)
if self.VERBOSE > 1 :
self.debug ("\nWriting issues due to `depends_on` or `needs` ...")
while self.pending :
(issue_id, issue) = self.pending.popitem ()
if issue_id not in self.processed :
if self.VERBOSE > 2 :
self.debug ("Adding %s ... " % issue_id)
self.process_issue (issue, tree)
else :
if self.VERBOSE > 3 :
self.debug ("%s already included." % issue_id)
file = open (self.oname, "w")
ElementTree (tree).write (file, encoding = "utf-8")
if self.VERBOSE > 1 :
self.debug ("Done.")
def requestMonitorId(self,monitorTag):
req = urllib2.Request(str('{0}/?apikey={1}&output={2}'+\
'&version={3}&action=getMonitors&tag={4}')\
.format(self.url,self.apiKey,self.output,self.version,monitorTag))
res = urllib2.urlopen(req)
xml = res.read()
root = ElementTree(file=StringIO.StringIO(xml)).getroot()
return root.find('./monitor/id').text
def loadBlissLexicon(fname):
from elementtree.ElementTree import ElementTree
xml = ElementTree(file=gOpenIn(fname))
pronunciations = pronunciationsFromXmlLexicon(xml)
result = [(orth, phon) for orth in pronunciations
if not (orth.startswith('[') and orth.endswith(']'))
for phon in pronunciations[orth]]
result.sort()
return result
def install_xpi(self, filename):
extract_path = os.path.join(self.profiledir, 'extensions', os.path.basename(filename))
os.makedirs(extract_path)
z = zipfile.ZipFile(filename, 'r')
z.extractall(extract_path)
doc = ElementTree(file = os.path.join(extract_path, 'install.rdf'))
eid = doc.find('.//{http://www.mozilla.org/2004/em-rdf#}id').text
os.rename(extract_path, os.path.join(os.path.dirname(extract_path), eid))
def tostring(node, *args, **kwds):
if 'pretty' in kwds or 'pretty_print' in kwds:
if 'pretty' in kwds: del kwds['pretty']
if 'pretty_print' in kwds: del kwds['pretty_print']
indent(node)
kwds.pop('pretty', None)
kwds.pop('pretty_print', None)
oss = StringIO()
ElementTree(node).write(oss, *args, **kwds)
return oss.getvalue()
def createXmlFile(filePath, rootElement, version='1.0', encoding=ENCODING_IN):
"""
Create an xml file
"""
doc = ElementTree(rootElement)
outfile = open(filePath, 'w')
outfile.write('<?xml version="' + version + '" encoding="' + encoding +
'" ?>')
doc._write(outfile, doc._root, ENCODING_IN, {})
outfile.close()
def process(self, lang):
assert len(lang) == 2, 'Language name must be two letters long'
doc = ElementTree(file='%s.xml' % lang)
root = doc.getroot()
if root.tag == 'resources':
for child in root:
self.walk(child, (child.get('name'), ), lang)
def gettemp():
cmd = ["omreport", "chassis", "temps", "-fmt", "xml"]
(omstdin, omstdout) = popen2.popen2(cmd)
tree = ElementTree()
root = tree.parse(omstdin)
iter = root.getiterator()
sensors = []
for element in iter:
if element.tag == "TemperatureProbe":
sensors.append(tempprobe(element))
return sensors
def listMonitors(self):
ret = list()
req = urllib2.Request(str('{0}/?apikey={1}&output={2}'+\
'&version={3}&action=getMonitors')\
.format(self.url,self.apiKey,self.output,self.version))
res = urllib2.urlopen(req)
xml = res.read()
root = ElementTree(file=StringIO.StringIO(xml)).getroot()
for monitor in list(root):
ret.append((monitor.find('id').text,monitor.find('tag').text,
monitor.find('name').text))
return ret
def xml_to_dict(fPath):
'''
Converts study data from (ref man generated) XML to a dictionary matching study IDs (keys) to
title/abstract tuples (values). For example: dict[n] might map to a tuple [t_n, a_n] where t_n is the
title of the nth paper and a_n is the abstract
'''
ref_ids_to_abs = {}
num_no_abs = 0
tree = ElementTree(file=fPath)
for record in tree.findall('.//record'):
pubmed_id = None
refmanid = eval(record.findtext('.//rec-number'))
# attempt to grab the pubmed id
pubmed_id = ""
try:
pubmed = record.findtext('.//notes/style')
pubmed = pubmed.split("-")
for i in range(len(pubmed)):
if "UI" in pubmed[i]:
pubmed_str = pubmed[i + 1].strip()
pubmed_id = eval("".join(
[x for x in pubmed_str if x in string.digits]))
except Exception, ex:
print "problem getting pmid ..."
print ex
ab_text = record.findtext('.//abstract/style')
if ab_text is None:
num_no_abs += 1
title_text = record.findtext('.//titles/title/style')
# Also grab keywords
keywords = [
keyword.text.strip().lower()
for keyword in record.findall(".//keywords/keyword/style")
]
# and authors
authors = [
author.text for author in record.findall(
".//contributors/authors/author/style")
]
# journal
journal = record.findtext(".//periodical/abbr-1/style")
ref_ids_to_abs[refmanid] = {"title":title_text, "abstract":ab_text, "journal":journal,\
"keywords":keywords, "pmid":pubmed_id, "authors":authors}
def PrintStats():
"""Looks at the XML output and dumps render time."""
try:
from elementtree.ElementTree import ElementTree
except:
print "Unable to load ElementTree, skipping statistics."
else:
doc = ElementTree(file='stats.xml')
for timer in doc.findall('//timer'):
if "totaltime" == timer.get("name"):
print "Render time was %s seconds" % timer[0].text
break
def gencix(major, minor):
# First generate first pass at the CILE over all of the lib tree
cixfile = "activeperl-%d.%d.cix" % (major, minor)
command = "python ../../../ci2.py scan -n -r -p -l Perl -T /tmp/ActivePerl-%d.%d/perl/lib -i \"*.pm\"> %s" % (
major, minor, cixfile)
retval = os.system(command)
if retval != 0:
print "Error scanning ActivePerl library"
sys.exit(retval)
#
# Grab the output of that scan
root = parse(cixfile).getroot()
newroot = Element("codeintel", version="2.0")
cixfile = SubElement(newroot,
"file",
lang="Perl",
mtime=str(int(time.time())),
path=os.path.basename('perl.cix'))
for file in root.getiterator('file'):
print >> sys.stderr, "Processing", file.get('path')
for blob in file:
if blob.get("src"):
# Don't want the src string.
del blob.attrib["src"]
cixfile.append(blob)
cix = genPerlStdCIX(
cixfile,
"/tmp/ActivePerl-%d.%d/perl/lib/pod/perlfunc.pod" % (major, minor))
parent_map = dict((c, p) for p in cixfile.getiterator() for c in p)
for variable in newroot.getiterator('variable'):
attributes = variable.get('attributes')
if attributes and '__local__' in variable.get('attributes'):
parent_map[variable].remove(variable)
# Generate the CIX.
print >> sys.stderr, "Prettying"
prettify(newroot)
tree = ElementTree(newroot)
#fname = '../../../lib/codeintel2/stdlibs/perl-%d.%d.cix' % (major, minor)
fname = 'perl-%d.%d.cix' % (major, minor)
#os.system('p4 edit %s' % fname)
stream = open(fname, "w")
print >> sys.stderr, "Writing"
stream.write('<?xml version="1.0" encoding="UTF-8"?>\n')
tree.write(stream)
stream.close()
def getpdisks(controller="0"):
cmd = [
"omreport", "storage", "pdisk", "controller=" + controller, "-fmt",
"xml"
]
(omstdin, omstdout) = popen2.popen2(cmd)
tree = ElementTree()
root = tree.parse(omstdin)
iter = root.getiterator()
pdisks = []
for element in iter:
if element.tag == "DCStorageObject":
pdisks.append(pdisk(element))
return pdisks
def dump(self, output, lang):
tempo = {}
root = Element('resources')
root.tail = '\n'
tempo[()] = root
for key in self._resources_order:
for i in range(1, len(key) + 1):
if key[0:i] not in tempo:
parent = tempo[key[0:i - 1]]
value = self._resources.get(key[0:i], None)
if value is None:
elem = SubElement(parent, 'node', name=key[i - 1])
else:
localized = value.get(lang, None)
english = value.get('en', None)
if english is None:
print >> sys.stderr, 'English file does not have the string for', key[
0:i]
print >> sys.stderr, ' entry is marked as obosolete.'
elem = SubElement(parent,
'node',
name=key[i - 1],
value=localized,
obsolete='true')
elif localized is not None:
elem = SubElement(parent,
'node',
name=key[i - 1],
value=localized)
else:
elem = SubElement(parent,
'node',
name=key[i - 1],
value=english,
toBeTranslated='true')
parent.text = elem.tail = '\n' + i * SPACES
tempo[key[0:i]] = elem
fix_it(root)
print >> output, '<?xml version="1.0" encoding="UTF-8"?>'
ElementTree(root).write(output, 'utf-8')
def getpower():
cmd = ["omreport", "chassis", "pwrsupplies", "-fmt", "xml"]
(omstdin, omstdout) = popen2.popen2(cmd)
tree = ElementTree()
root = tree.parse(omstdin)
iter = root.getiterator()
status = ""
pwrsupplies = []
for element in iter:
if element.tag == "Redundancy":
status = element.get("status")
redunstatus = element.findtext("RedunStatus")
if element.tag == "PowerSupply":
pwrsupplies.append(powersupply(element))
return [(status, redunstatus), pwrsupplies]
def GetElementsFromXML(self, filename):
'Extracts a dictionary of elements from the gcc_xml file.'
tree = ElementTree()
try:
tree.parse(filename)
except ExpatError:
raise InvalidXMLError, 'Not a XML file: %s' % filename
root = tree.getroot()
if root.tag != 'GCC_XML':
raise InvalidXMLError, 'Not a valid GCC_XML file'
# build a dictionary of id -> element, None
elementlist = root.getchildren()
elements = {}
for element in elementlist:
id = element.get('id')
if id:
elements[id] = element, None
return elements
def currency_data(
self,
xml_url='http://www.ecb.europa.eu/stats/eurofxref/eurofxref-hist-90d.xml'
):
"""Returns the most recent currency data with tuples."""
now = datetime.now()
today = u'-'.join(
[unicode(now.year),
unicode(now.month),
unicode(now.day)])
if today == self.updated_date():
return
etree90 = ElementTree()
try:
data90 = urllib2.urlopen(xml_url)
root90 = ElementTree.parse(etree90, data90)
DATA90 = root90[2]
DATA_list = []
for DATA in DATA90:
daily_data_list = []
for daily_data in DATA:
daily_data_tuple = (daily_data.get('currency'),
daily_data.get('rate'))
daily_data_list.append(daily_data_tuple)
ddl = (DATA.get('time'), dict(daily_data_list))
DATA_list.append(ddl)
date = DATA_list[0][0]
try:
if self.date != date:
self.currencies = DATA_list
self.date = date
for date in self.currencies:
for key in date[1].keys():
if key not in self.codes:
self.codes.append(key)
self.amount_of_days = range(1, len(self.currencies) + 1)
except AttributeError:
self.currencies = DATA_list
except:
pass
def test():
import sys
doc = HTML(HEAD('ankjwajhsjasa', META('blabal')))
table = TABLE()
body = BODY(
table.append(
TBODY('ahasa', TR(
TD('blabla'),
TD('blabla'),
TD('blabla'),
))))
p1, p2 = P('blabla'), P('bli')
p2.text += 'dhsdhshkds'
doc += body
doc += (p1, p2)
tree = ElementTree(doc)
write_pretty(tree, sys.stdout)
def __init__(self, lstData, GeoType, strPath, strFilename, strLayername):
dctWriteKML = {'Point': self.writePoint, 'Polyline': self.writeLine, 'Polygon': self.writePolygon}
#Create new element tree with a root of KML...
objRoot = Element("{http://earth.google.com/kml/2.1}kml")
objTree = ElementTree(element=objRoot)
elemDoc = SubElement(objRoot, 'Document')
elemDocName = SubElement(elemDoc, 'name')
#According the KML spec, default Polystyle stuff goes here...
elemDocName.text = strLayername
#Add a document name element here...populate from supplied parameters
for objRow in lstData:
elemPlace = SubElement(elemDoc, 'Placemark')
elemName =SubElement(elemPlace,'name')
elemName.text = objRow['Name']
#Add support for the description tag...
elemDesc = SubElement(elemPlace, 'description')
elemDesc.text = objRow['Description']
elemGeo = dctWriteKML.get(GeoType, self.errHandler)(objRow['Geometry'], elemPlace)
elemPlace.append(elemGeo)
self.Write(objTree, strPath, strFilename)
def output_workers (self, file = sys.stdout) :
week = []
tree = Element ("resources-list", type = "worker")
tt = SubElement (tree, "timetable", id = "weekend")
SubElement (tt, "dayoff", type = "weekday").text = "saturday"
SubElement (tt, "dayoff", type = "weekday").text = "sunday"
for day in ("monday", "tuesday", "wednesday", "thursday", "friday") :
tt = SubElement (tree, "timetable", id = day)
SubElement (tt, "dayoff", type = "weekday").text = day
week.append (day)
stati = [self.db.user_status.lookup (i)
for i in ("valid", "obsolete", "system")
]
for uid in self.db.user.filter (None, dict (status = stati)) :
dyn = self.get_user_dynamic (self.db, uid, self.now)
if not dyn :
dyn = self.last_user_dynamic (self.db, uid)
user = self.db.user.getnode (uid)
if not user.nickname and not user.username :
continue
r = SubElement \
( tree
, "resource"
, id = (user.nickname or user.username).decode ("utf-8")
, fullname = (user.realname or user.username).decode ("utf-8")
)
SubElement (r, "use-timetable", idref = "weekend")
wh = 38.5
if dyn :
wh = self.weekly_hours (dyn) or 38.5
wh *= 4
wh += 7.75 * 4 - 1
wh = int (wh)
wh = int (wh / (7.75 * 4))
for i in range (wh, 5) :
SubElement (r, "use-timetable", idref = week [i])
ElementTree (tree).write (file, encoding = "utf-8")
import sys
from elementtree.ElementTree import ElementTree
mydoc = ElementTree(file=sys.argv[1])
for e in mydoc.findall(sys.argv[2]):
print e.text
def xml_to_dict(fpath):
'''
Converts study data from (ref man generated) XML to a dictionary matching study IDs (keys) to
title/abstract tuples (values). For example: dict[n] might map to a tuple [t_n, a_n] where t_n is the
title of the nth paper and a_n is the abstract
'''
ref_ids_to_abs = {}
parsing_errors = []
num_no_abs = 0
tree = ElementTree(file=fpath)
num_failed = 0
for record in tree.findall('.//record'):
pubmed_id, refmanid = None, None
refman_version = record.findtext('.//source-app')
path_str = None
### here we check the RefMan version, and change
# the xml path accordingly. this fixes issue #7
if refman_version == 'Reference Manager 12.0':
path_str = './/rec-number/style'
journal_path_str = './/periodical/full-title/style'
elif refman_version == 'Reference Manager 11.0':
path_str = './/rec-number'
journal_path_str = './/periodical/abbr-1/style'
try:
refmanid = int(record.findtext(path_str))
except:
error = "Unable to parse record '%s' in '%s'" % (
record, os.path.basename(fpath))
#print "failed to parse refman document"
parsing_errors.append(error)
if refmanid is not None:
# attempt to grab the pubmed id
pubmed_id = ""
try:
pubmed = record.findtext('.//notes/style')
pubmed = pubmed.split("-")
for i in range(len(pubmed)):
if "UI" in pubmed[i]:
pubmed_str = pubmed[i + 1].strip()
pubmed_id = int("".join(
[x for x in pubmed_str if x in string.digits]))
except Exception, ex:
error = "Problem getting pmid from '%s' in '%s'" % (
record, os.path.basename(fpath))
parsing_errors.append(error)
#print "problem getting pmid ..."
#print ex
#print("\n")
ab_text = record.findtext('.//abstract/style')
if ab_text is None:
num_no_abs += 1
title_text = record.findtext('.//titles/title/style')
# Also grab keywords
keywords = [
keyword.text.strip().lower()
for keyword in record.findall(".//keywords/keyword/style")
]
# and authors
authors = [
author.text for author in record.findall(
".//contributors/authors/author/style")
]
# journal
journal = record.findtext(journal_path_str)
ref_ids_to_abs[refmanid] = {"title":title_text, "abstract":ab_text, "journal":journal,\
"keywords":keywords, "pmid":pubmed_id, "authors":authors}
from elementtree.ElementTree import Element, ElementTree, SubElement
_src_f = open("pycon_src.xml")
_content = _src_f.read()
_src_f.close()
_content = _content.replace("<description>", "<description>\n<![CDATA[\n")
_content = _content.replace("</description>", "\n\n\n]]>\n</description>")
_content = _content.replace("<", "<")
_content = _content.replace(">", ">")
_tmp_f = open("pycon_src_tmp.xml", "wb")
_tmp_f.write(_content)
_tmp_f.close()
_src_xml = ElementTree(file="pycon_src_tmp.xml")
_root = Element("xml")
_conference = SubElement(_root, "conference")
# add pyconfr main values
SubElement(_conference, "title").text = "PyCONFR 2010"
SubElement(_conference, "subtitle").text = \
"Rendez-vous annuel des utilisateurs de Python organisee par l'Association Francophone Python"
SubElement(_conference, "venue").text = "Cyberbase de la Cite des Sciences"
SubElement(_conference, "city").text = "Paris"
SubElement(_conference, "start").text = "2010-10-28"
SubElement(_conference, "end").text = "2010-10-29"
SubElement(_conference, "days").text = "2"
SubElement(_conference, "day_change").text = "08:00"
def main(options, args):
# 1. load reference lexicon
print('loading reference lexicon ...')
lexicon = loadBlissLexicon(options.lexicon)
knownWords = set([ orth for orth, phon in lexicon ])
# 2. load model for fragmentizing unknown words
if options.subliminal_lexicon:
print('loading subliminal lexicon ...')
subliminalLexicon = loadBlissLexicon(options.subliminal_lexicon)
else:
subliminalLexicon = None
if options.subliminal_g2p:
print('loading subliminal g2p model ...')
subliminalG2p = pickle.load(open(options.subliminal_g2p))
else:
subliminalG2p = None
if options.g2pModel:
print('loading g2p model ...')
model = pickle.load(open(options.g2pModel))
oldSize, newSize = model.strip()
print('stripped number of multigrams from %d to %d' % (oldSize, newSize))
fragmentizer = Fragmentizer(model)
if subliminalLexicon:
fragmentizer.addSupervised(subliminalLexicon)
if subliminalG2p:
fragmentizer.addSupervised(subliminalG2p)
graphones = model.sequitur.symbols()
graphones.remove(model.sequitur.symbol(model.sequitur.term))
else:
model = fragmentizer = graphones = None
# 3. add fragments to lexicon
if options.write_lexicon:
print('creating extended lexicon ...')
xmlLexicon = ElementTree(file = options.lexicon)
if options.model_type == 'phonemes':
changeSyntaticToPhonetic(xmlLexicon)
else:
addGraphonesToLexicon(xmlLexicon, graphones)
xmlLexicon.write(gOpenOut(options.write_lexicon), defaultEncoding)
# 4. determine set of LM tokens
vocabulary = mGramCounts.ClosedVocablary()
vocabulary.add(['<s>', '</s>'])
if options.model_type == 'flat-hybrid':
vocabulary.add(filter(isLmToken, knownWords), soft=True)
if graphones:
vocabulary.add(starmap(lmToken, graphones))
vocabulary.sort()
if options.write_tokens:
f = gOpenOut(options.write_tokens, defaultEncoding)
if options.model_type == 'phonemes':
phonemes = set(p for orth, phon in lexicon for p in phon)
phonemes.add('#1')
if 'si' in phonemes: phonemes.remove('si')
for p in sorted(phonemes):
print(p, file=f)
else:
for w in vocabulary:
if w is not None:
print(w, file=f)
# 5./6. set-up LM event generator
if options.write_counts or options.write_events:
order = options.order - 1
if options.model_type == 'flat-hybrid':
events = HybridEventGenerator(knownWords, fragmentizer, order)
if options.range_type == 'fragments':
events.setFragmentRange()
elif options.range_type == 'words':
events.setTrueWordRange()
else:
assert ValueError(options.range_type)
elif options.model_type == 'fragments':
events = OovEventGenerator(knownWords, fragmentizer, order)
elif options.model_type == 'phonemes':
events = PhonemeEventGenerator(lexicon, order)
# 5. create modified LM training corpus counts
if options.write_events:
print('creating sequence model events ...')
f = gOpenOut(options.write_events, defaultEncoding)
for event, count in events(gOpenIn(options.text, defaultEncoding)):
print(repr(event), '\t', count, file=f)
# 6. count LM events
if options.write_counts:
print('creating sequence model counts ...')
counts = mGramCounts.SimpleMultifileStorage()
counts.addIter(events(gOpenIn(options.text, defaultEncoding)))
mGramCounts.TextStorage.write(gOpenOut(options.write_counts, defaultEncoding), counts)
# 7. dump list of OOV words and their corresponding fragmentation
if options.write_fragments:
print('dumping fragments ...')
f = gOpenOut(options.write_fragments, defaultEncoding)
events = OovFragmentGenerator(knownWords, fragmentizer)
fragments = events(gOpenIn(options.text, defaultEncoding))
for event in list(fragments.keys()):
print(event, '\t', ' '.join(fragments[event]), file=f)
# 8. dump modified LM training text
if options.write_lm_text:
print('dumping modified LM training text ...')
f = gOpenOut(options.write_lm_text, defaultEncoding)
events = OovFragmentGenerator(knownWords, fragmentizer)
for line in gOpenIn(options.text, defaultEncoding):
words = line.split()
modWords = events.modifyLmText(words)
print(" ".join(modWords), file=f)
<author>
<name>John Doe</name>
</author>
<id>urn:uuid:60a76c80-d399-11d9-b93C-0003939e0af6</id>
<entry>
<title type="xhtml">Atom-Powered <br/> Robots Run Amok</title>
<link href="http://example.org/2003/12/13/atom03"/>
<id>urn:uuid:1225c695-cfb8-4ebb-aaaa-80da344efa6a</id>
<updated>2003-12-13T18:30:02Z</updated>
<summary>Some text.</summary>
</entry>
</feed>"""
etree = ElementTree(file=StringIO.StringIO(content))
feed = XML(content)
print etree
print feed
#print len(feed)
#print feed[0]
#print feed.keys()
ATOM = "http://www.w3.org/2005/Atom"
entry = etree.getiterator('{%s}entry'%ATOM)[0]
new_lin = SubElement(entry, '{%s}link'%ATOM)
new_lin.set('rel', 'source')
new_lin.set('href', 'http://somthing.org')
def xmlToDict(fPath, stopPath=None, splitTxt= False, get_pubmed = False):
'''
Converts study data from (ref man generated) XML to a dictionary matching study IDs (keys) to
title/abstract tuples (values). For example: dict[n] might map to a tuple [t_n, a_n] where t_n is the
title of the nth paper and a_n is the abstract
'''
refIDToAbs = {}
numNoPubmeds = 0
numNoAbs = 0 # Keep track of how many studies have no abstracts.
tree = ElementTree(file=fPath)
for record in tree.findall('.//record'):
pubmed_id = None
refmanid = eval(record.findall('.//rec-number')[0].text)
try:
pubmed = record.findall('.//notes/style')[0].text
pubmed = pubmed.split("-")
for i in range(len(pubmed)):
if "UI" in pubmed[i]:
pubmed_str = pubmed[i+1].strip()
pubmed_id = eval("".join([x for x in pubmed_str if x in string.digits]))
#pubmed_id = eval(pubmed[i+1].replace("PT", "").replace("IN", ""))
#print pubmed
break
except Exception, ex:
print ex
if pubmed_id is None:
#if not "Cochrane" in pubmed[2]:
# pdb.set_trace()
numNoPubmeds+=1
print "%s has no pubmed id" % refmanid
abstract = record.findall('.//abstract/style')
abText = ""
try:
if abstract and splitTxt:
abText = (abstract[0].text).split(" ")
abText = [string.lower(s) for s in abText]
abText = cleanUpTxt(abText, stopListPath=stopPath)
elif abstract:
abText = abstract[0].text
else:
numNoAbs += 1
except:
pdb.set_trace()
title = ""
if splitTxt:
title = cleanUpTxt(string.lower(record.findall('.//titles/title/style')[0].text).split(" "), stopListPath=stopPath)
else:
try:
title = record.findall('.//titles/title/style')[0].text
except:
pdb.set_trace()
# Also grab keywords
keywords = [keyword.text.strip().lower() for keyword in record.findall(".//keywords/keyword/style")]
if pubmed_id is not None or True:
refIDToAbs[refmanid] = [title, abText, keywords, pubmed_id]
def genPerlStdCIX(filename, stream):
log.debug("genPerlStdCIX(filename=%r, stream=%r)", filename, stream)
root = Element("codeintel", version="2.0")
cixfile = SubElement(root,
"file",
lang="Perl",
mtime=str(int(time.time())),
path=os.path.basename(filename))
# Process Perl's built-ins out of perlfunc.pod.
if 1:
p4path = "//depot/main/Apps/Gecko/src/Core/pod/perlfunc.pod"
cmd = "p4 print -q %s" % p4path
i, o, e = os.popen3(cmd)
lines = o.read().splitlines(0)
i.close()
o.close()
retval = e.close()
if retval:
raise Error("error running: %s" % cmd)
else:
lines = open("perlfunc.pod", 'r').read().splitlines(0)
# Parse the "Alphabetical Listing of Perl Functions" into a list of
# 'blocks' where each block is one command-"=item" block.
start = lines.index("=head2 Alphabetical Listing of Perl Functions")
blocks = []
block = None
level = 0
def parseItem(line):
sig = line.split(None, 1)[1]
name = re.split("[ \t\n(/]", sig, 1)[0]
return name, sig
for i, line in enumerate(lines[start:]):
if line.startswith("=over"):
level += 1
if line.startswith("=back"):
level -= 1
if level == 0: # done the 'Alphabetical Listing' section
if block:
blocks.append(block)
break
if level > 1:
if block:
block["lines"].append(line)
elif block is None and not line.startswith("=item"):
continue
elif block is None and line.startswith("=item"):
block = {}
name, sig = parseItem(line)
block = {"name": name, "sigs": [sig], "lines": []}
elif line.startswith("=item"):
name, sig = parseItem(line)
if name == block["name"]:
block["sigs"].append(sig)
else:
blocks.append(block)
block = {"name": name, "sigs": [sig], "lines": []}
else:
if not block["lines"] and not line.strip():
pass # drop leading empty lines
elif not line.strip() and block["lines"] and \
not block["lines"][-1].strip():
pass # collapse multiple blank lines
else:
block["lines"].append(line)
# pprint(blocks)
# Process the blocks into a list of command info dicts.
def podrender(pod):
rendered = pod
rendered = re.sub("F<(.*?)>", r"\1", rendered)
rendered = re.sub("I<(.*?)>", r"*\1*", rendered)
def quoteifspaced(match):
if ' ' in match.group(1):
return "'%s'" % match.group(1)
else:
return match.group(1)
rendered = re.sub("C<(.*?)>", quoteifspaced, rendered)
def linkrepl(match):
content = match.group(1)
if content.startswith("/"):
content = content[1:]
if "/" in content:
page, section = content.split("/", 1)
content = "%s in '%s'" % (section, page)
else:
content = "'%s'" % content
return content
rendered = re.sub("L<(.*?)>", linkrepl, rendered)
return rendered
# These perl built-ins are grouped in perlfunc.pod.
commands = []
WIDTH = 60 # desc field width
syscalls = """
getpwnam getgrnam gethostbyname getnetbyname getprotobyname
getpwuid getgrgid getservbyname gethostbyaddr getnetbyaddr
getprotobynumber getservbyport getpwent getgrent gethostent
getnetent getprotoent getservent setpwent setgrent sethostent
setnetent setprotoent setservent endpwent endgrent endhostent
endnetent endprotoent endservent
""".split()
calltip_skips = "sub use require".split()
for block in blocks:
name, sigs, lines = block["name"], block["sigs"], block["lines"]
if name == "-X": # template for -r, -w, -f, ...
pattern = re.compile(r"^ (-\w)\t(.*)$")
tlines = [line for line in lines if pattern.match(line)]
for tline in tlines:
tname, tdesc = pattern.match(tline).groups()
tsigs = [s.replace("-X", tname) for s in sigs]
command = {
"name": tname,
"sigs": tsigs,
"desc": textwrap.fill(tdesc, WIDTH)
}
commands.append(command)
elif name in ("m", "q", "qq", "qr", "qx", "qw", "s", "tr", "y"):
operators = {
"m":
"""\
m/PATTERN/cgimosx
/PATTERN/cgimosx
Searches a string for a pattern match, and in scalar
context returns true if it succeeds, false if it fails.
""",
"q":
"""\
q/STRING/
'STRING'
A single-quoted, literal string.
""",
"qq":
"""\
qq/STRING/
"STRING"
A double-quoted, interpolated string.
""",
"qr":
"""\
qr/STRING/imosx
Quotes (and possibly compiles) STRING as a regular
expression.
""",
"qx":
"""\
qx/STRING/
`STRING`
A string which is (possibly) interpolated and then
executed as a system command.
""",
"qw":
"""\
qw/STRING/
Evaluates to a list of the words extracted out of STRING,
using embedded whitespace as the word delimiters.
""",
"s":
"""\
s/PATTERN/REPLACEMENT/egimosx
Searches a string for a pattern, and if found, replaces
that pattern with the replacement text and returns the
number of substitutions made. Otherwise it returns the
empty string.
""",
"tr":
"""\
tr/SEARCHLIST/REPLACEMENTLIST/cds
y/SEARCHLIST/REPLACEMENTLIST/cds
Transliterates all occurrences of the characters found in
the search list with the corresponding character in the
replacement list. It returns the number of characters
replaced or deleted.
""",
"y":
"""\
tr/SEARCHLIST/REPLACEMENTLIST/cds
y/SEARCHLIST/REPLACEMENTLIST/cds
Transliterates all occurrences of the characters found in
the search list with the corresponding character in the
replacement list. It returns the number of characters
replaced or deleted.
""",
}
sigs = []
desclines = None
for line in operators[name].splitlines(0):
if desclines is not None:
desclines.append(line.strip())
elif not line.strip():
desclines = []
else:
sigs.append(line.strip())
command = {
"name": name,
"sigs": sigs,
"desc": textwrap.fill(' '.join(desclines), WIDTH)
}
commands.append(command)
elif name in syscalls:
desc = "Performs the same function as the '%s' system call." % name
desc = textwrap.fill(desc, WIDTH)
getterListContext = {
"getpw": "\n"
" ($name,$passwd,$uid,$gid,$quota,$comment,\n"
" $gcos,$dir,$shell,$expire) = %s",
"getgr": "\n ($name,$passwd,$gid,$members) = %s",
"gethost":
"\n ($name,$aliases,$addrtype,$length,@addrs) = %s",
"getnet": "\n ($name,$aliases,$addrtype,$net) = %s",
"getproto": "\n ($name,$aliases,$proto) = %s",
"getserv": "\n ($name,$aliases,$port,$proto) = %s",
}
getterScalarContext = {
"getgrent": "$name = %s",
"getgrgid": "$name = %s",
"getgrnam": "$gid = %s",
"gethostbyaddr": "$name = %s",
"gethostbyname": "$addr = %s",
"gethostent": "$name = %s",
"getnetbyaddr": "$name = %s",
"getnetbyname": "$net = %s",
"getnetent": "$name = %s",
"getprotobyname": "$num = %s",
"getprotobynumber": "$name = %s",
"getprotoent": "$name = %s",
"getpwent": "$name = %s",
"getpwnam": "$uid = %s",
"getpwuid": "$name = %s",
"getservbyname": "$num = %s",
"getservbyport": "$name = %s",
"getservent": "$name = %s",
}
for prefix, template in getterListContext.items():
if name.startswith(prefix):
desc += template % sigs[0]
if name in getterScalarContext:
desc += "\nin list context or:\n "\
+ getterScalarContext[name] % sigs[0]
command = {"name": name, "desc": desc, "sigs": sigs}
commands.append(command)
elif name == "shmread":
desc = """\
Reads the System V shared memory segment ID
starting at position POS for size SIZE by attaching to it,
copying out, and detaching from it.
"""
desc = ' '.join([ln.strip() for ln in desc.splitlines(0)])
command = {
"name": name,
"sigs": sigs,
"desc": textwrap.fill(desc, WIDTH)
}
commands.append(command)
elif name == "shmwrite":
desc = """\
Writes the System V shared memory segment ID
starting at position POS for size SIZE by attaching to it,
copying in, and detaching from it.
"""
desc = ' '.join([ln.strip() for ln in desc.splitlines(0)])
command = {
"name": name,
"sigs": sigs,
"desc": textwrap.fill(desc, WIDTH)
}
commands.append(command)
elif name in calltip_skips:
continue # just drop the sub calltip: annoying
else:
# Parsing the description from the full description:
# Pull out the first sentence up to a maximum of three lines
# and one paragraph. If the first *two* sentences fit on the
# first line, then use both.
desc = ""
sentencePat = re.compile(r"([^\.]+(?:\. |\.$))")
if name in ("dbmclose", "dbmopen"):
# Skip the first paragraph: "[This function...superceded by"
lines = lines[lines.index('') + 1:]
elif name == "do":
# Skip the first sentence: "Not really a function."
end = sentencePat.match(lines[0]).span()[1]
lines[0] = lines[0][end:].lstrip()
for i, line in enumerate(lines):
if not line.strip():
break
sentences = sentencePat.findall(line)
if not sentences:
desc += line + ' '
continue
elif i == 0 and len(sentences) > 1:
desc += ' '.join([s.strip() for s in sentences[:2]])
else:
desc += sentences[0].strip()
break
command = {
"name": name,
"sigs": sigs,
"desc": textwrap.fill(podrender(desc), WIDTH)
}
commands.append(command)
# for command in commands:
# print
# print banner(command["name"], '-')
# print '\n'.join(command["sigs"])
# print
# print command["desc"]
# Generate the CIX for each function.
module_elt = SubElement(cixfile, "scope", ilk="blob",
name="*") # "built-ins" module
for command in commands:
name, sigs, desc = command["name"], command["sigs"], command["desc"]
func_elt = SubElement(module_elt, "scope", ilk="function", name=name)
if sigs:
func_elt.set("signature", '\n'.join(sigs))
if desc:
doclines = desc.split('\n')[:3]
# doclines = parseDocSummary(doclines)
doc = '\n'.join(doclines)
func_elt.set("doc", doc)
# Generate the CIX.
prettify(root)
tree = ElementTree(root)
stream.write('<?xml version="1.0" encoding="UTF-8"?>\n')
tree.write(stream)
