def make_node_page(self, ident):
global g_paths
tb = et.TreeBuilder()
if ident:
index_attribs = {"title": self._make_title(ident, True),
"ident": ".".join(self.fcm.get_pslcode(ident)),
"version": self.versionstring}
filename = self._make_href(ident)
else: #contents page
index_attribs = {"title": "Contents",
"version": self.versionstring}
filename = "index.html"
tb.start("index", index_attribs)
if not ident:#inject revisions list link into index.html
tb.start("page", {"href": "revisions.html"})
tb.data("Revision list")
tb.end("page")
for i in self.fcm.get_children(ident):
self._recursive_add_index_section(i, tb)
tb.end("index")
page_string= subprocess.Popen(["xsltproc", "--nonet", "--novalid", g_paths.xsldir + "index.xsl", "-"],
stdin=subprocess.PIPE, stdout=subprocess.PIPE
).communicate(et.tostring(tb.close(), "utf-8"))[0]
page_string = page_string.replace("<!--linkbar-->", self._build_linkbar(ident))
print "Creating", filename
of = open(g_paths.html_output + filename, "w")
of.write(page_string)
def save(self):
save = cElementTree.TreeBuilder()
save.start('correcting-session')
self._save_session(save)
xml_str = cElementTree.tostring(save.end('correcting-session'))
with open(self.__session_file(), 'bw+') as session_file:
session_file.write(xml_str)
def __init__(self, filename=None, run=None, overwrite=False):
cElementTree.register_namespace("", "http://psi.hupo.org/ms/mzml")
self.filename = filename
self.lookup = {}
self.newTree = None
self.TreeBuilder = cElementTree.TreeBuilder()
self.run = run
self.info = {'counters': ddict(int)}
if self.run.info['filename'].endswith('.gz'):
import gzip
import codecs
io = codecs.getreader("utf-8")(gzip.open(
self.run.info['filename']))
else:
io = open(self.run.info['filename'], 'r')
for event, element in cElementTree.iterparse(io,
events=(b'start',
b'end')):
if self.newTree == None:
self.newTree = cElementTree.Element(element.tag,
element.attrib)
if event == b'start' and element.tag.endswith("}mzML"):
self.TreeBuilder.start(element.tag, element.attrib)
else:
if event == b'start':
self.TreeBuilder.start(element.tag, element.attrib)
if element.tag.endswith('}run'):
self.lookup['run'] = cElementTree.Element(
element.tag, element.attrib)
if element.tag.endswith('}spectrumList'):
self.lookup['spectrumList'] = cElementTree.Element(
element.tag, element.attrib)
self.lookup['spectrumIndeces'] = cElementTree.Element(
'index', {'name': 'spectrum'}),
break
elif element.tag.endswith('}chromatogramList'):
break
else:
pass
else:
if element.tag.endswith('}softwareList'):
### Insert pymzML software tag
## Example :software id="pwiz_Reader_Thermo"><softwareParam accession="MS:1000615" cvRef="MS" name="ProteoWizard" version="1.0" />
self.TreeBuilder.start('software',
{'id': 'pymzML 0.7.1'})
self.TreeBuilder.start(
'softwareParam', {
'accession': 'MS:0000000',
'cvRef': 'MS',
'name': 'pymzML writer',
'version': '0.7.1'
})
self.newTree.append(
self.TreeBuilder.end('softwareParam'))
self.newTree.append(self.TreeBuilder.end('software'))
self.TreeBuilder.data(element.text)
self.newTree.append(self.TreeBuilder.end(element.tag))
return
def obj_to_doc(obj, *args, **kwargs):
"""Convert an object to am XML document object
:rtype: xml.etree.ElementTree.Element
"""
builder = ET.TreeBuilder()
obj.build(builder, *args, **kwargs)
return builder.close()
def WriteQhp(symbols, files, qhp_filename):
builder = ElementTree.TreeBuilder()
with Element(builder, "QtHelpProject", {"version": "1.0"}):
Data(builder, "namespace", NAMESPACE)
Data(builder, "virtualFolder", "doc")
with Element(builder, "customFilter", {"name": FILTER_NAME}):
Data(builder, "filterAttribute", FILTER_ID)
Data(builder, "filterAttribute", VERSION)
with Element(builder, "filterSection"):
Data(builder, "filterAttribute", FILTER_ID)
Data(builder, "filterAttribute", VERSION)
with Element(builder, "toc"):
pass
with Element(builder, "keywords"):
for sym in symbols:
Data(builder,
"keyword",
args={
"name": sym.full_name,
"id": sym.full_name,
"ref": sym.filename
})
with Element(builder, "files"):
for filename in files:
Data(builder, "file", filename)
with open(qhp_filename, "w") as handle:
handle.write(ElementTree.tostring(builder.close()))
def fromstringlist(sequence, parser=None):
"""
Taken from Python2.7 source
"""
if not parser:
parser = ET.XMLParser(target=ET.TreeBuilder())
for text in sequence:
parser.feed(text)
return parser.close()
def make_revision_list(self):
global g_paths
print "Writing revision list"
tb = et.TreeBuilder()
tb.start("revisions", {"title": "Revision list",
"version": self.versionstring})
self._recursive_add_revision_node(tb, None)
tb.end("revisions")
page_string= subprocess.Popen(["xsltproc", "--nonet", "--novalid", g_paths.xsldir + "revisions.xsl", "-"],
stdin=subprocess.PIPE, stdout=subprocess.PIPE
).communicate(et.tostring(tb.close(), "utf-8"))[0]
page_string = page_string.replace("<!--linkbar-->", self._build_linkbar("REV"))
of = open(g_paths.html_output + "revisions.html", "w")
of.write(page_string)
def handle_starttag(self, tag, attrs):
if tag == 'a':
builder = etree.TreeBuilder()
builder.start(tag, dict(attrs))
builder.end(tag)
full_tag = builder.close()
self.link = {
'original_tag':
etree.tostring(full_tag).decode("utf-8").replace(' /', ''),
'url':
dict(attrs)['href'],
'text':
''
}
self.found_link = True
def WriteQhcp(qhp_filenames, qch_filenames, qhcp_filename):
builder = ElementTree.TreeBuilder()
with Element(builder, "QHelpCollectionProject", {"version": "1.0"}):
with Element(builder, "docFiles"):
with Element(builder, "generate"):
for i, filename in enumerate(qhp_filenames):
with Element(builder, "file"):
Data(builder, "input", filename)
Data(builder, "output", qch_filenames[i])
with Element(builder, "register"):
for filename in qch_filenames:
Data(builder, "file", filename)
with open(qhcp_filename, "w") as handle:
handle.write(ElementTree.tostring(builder.close()))
def parse_xml(self, xml_output):
"""
Open and parse an xml file.
TODO: Write custom parser to just read the nodes that we need instead of
reading the whole file.
@return xml_tree An xml tree instance. None if error.
"""
try:
parser = ET.XMLParser(target=ET.TreeBuilder())
parser.feed(xml_output)
tree = parser.close()
except SyntaxError as err:
print("SyntaxError: %s. %s" % (err, xml_output))
return None
return tree
def parse(file, builder=None, encoding=None):
bob = builder
def emit(soup):
if isinstance(soup, BS.NavigableString):
if isinstance(soup, ignorable_soup):
return
bob.data(unescape(soup))
else:
attrib = dict([(k, unescape(v)) for k, v in soup.attrs])
bob.start(soup.name, attrib)
for s in soup:
emit(s)
bob.end(soup.name)
# determine encoding (the document charset is not reliable)
try:
if not hasattr(file, "read"):
file = open(file)
text = file.read()
except:
text = file
if not encoding:
try:
encoding = "utf-8"
unicode(text, encoding)
except UnicodeError:
encoding = "iso-8859-1"
soup = BS.BeautifulSoup(text,
convertEntities="html",
fromEncoding=encoding)
# build the tree
if not bob:
bob = ET.TreeBuilder()
emit(soup)
root = bob.close()
# wrap the document in a html root element, if necessary
if len(root) == 1 and root[0].tag == "html":
return root[0]
root.tag = "html"
return root
def make_page(self, sid, prevsid, nextsid):
global g_paths
filename = self._make_href(sid)
print "Creating:", filename
tb = et.TreeBuilder()
revs = []
jsarray = []
page_attributes = {"title": self._make_title(sid, True),
"version": self.versionstring}
if prevsid:
page_attributes["prev"] = self._make_href(prevsid)
page_attributes["prevtitle"] = self._make_title(prevsid)
if nextsid:
page_attributes["next"] = self._make_href(nextsid)
page_attributes["nexttitle"] = self._make_title(nextsid)
tb.start("page", page_attributes)
self._recursive_build_node(tb, sid, jsarray=jsarray, revs=revs)
tb.end("page")
stylesheet_name = g_paths.xsldir + "page.xsl"
tf = None
if revs:
tf = self._make_temporary_stylesheet(stylesheet_name, revs)
stylesheet_name = tf.name
page_string= subprocess.Popen(["xsltproc", "--nonet", "--novalid", stylesheet_name, "-"],
stdin=subprocess.PIPE, stdout=subprocess.PIPE
).communicate(et.tostring(tb.close(), "utf-8"))[0]
if tf: os.unlink(tf.name)
#create javascript variables for controlling folding
page_string = page_string.replace(
"<!--jsvariable-->",
"var folding = " + str(jsarray) + ";")
#replace xml links with xhtml links
page_string = self._process_links(page_string)
#insert link bar
page_string = page_string.replace("<!--linkbar-->", self._build_linkbar(sid))
#convert cgm images to png images
page_string = re.sub("<img[^>]*></img>", self.cgmtopng, page_string)
#write the file
of = open(g_paths.html_output + filename, "w")
of.write(page_string)
def _build_linkbar(self, ident):
title_crop = 30
tb = et.TreeBuilder()
tb.start("div", {"class": "linkbar"})
tb.start("p", {})
if ident: #contents page passes in empty list
tb.start("a", {"title": "Contents",
"href": "index.html"})
tb.data("Contents")
tb.end("a")
if ident == "REV":
ident_list = []
else:
ident_list = self.fcm.get_ancestors(ident)
for i in ident_list:
tb.data(" >> ")
title = self._make_title(i)
tb.start("a", {"title": title,
"href": self._make_href(i)})
tb.data(title[:title_crop])
if len(title) > title_crop:
tb.data("...")
tb.end("a")
else:
tb.data(u" ")
tb.end("p")
tb.start("div", {"class": "otherlinks"})
tb.start("p", {})
tb.data(u"| ")
tb.start("a", {"href": "search.html"})
tb.data("Search")
tb.end("a")
tb.end("p")
tb.end("div")
tb.end("div")
return et.tostring(tb.close(), "utf-8")
def __init__(self):
super().__init__()
self.tb = etree.TreeBuilder(element_factory=H)
self.tb.start("root", {})
def __init__(self, target=None):
HTMLParser.__init__(self)
self.__builder = target or ET.TreeBuilder()
def __init__(self):
self.tree_builder = ET.TreeBuilder()
self.close = self.tree_builder.close
self.data = self.tree_builder.data
self.stack = []
def __init__(self, filename=None, run=None, overwrite=False):
cElementTree.register_namespace("", "http://psi.hupo.org/ms/mzml")
self.filename = filename
self.lookup = {}
self.newTree = None
self.TreeBuilder = cElementTree.TreeBuilder()
self.run = run
self.info = {'counters': ddict(int)}
if self.run.info['filename'].endswith('.gz'):
import gzip
import codecs
io = codecs.getreader("utf-8")(gzip.open(self.run.info['filename']))
else:
io = open(self.run.info['filename'], 'r')
#read the rest as original file
input_xml_string = ''
pymzml_tag_written = False
#open again to read as text!
for line in open(self.run.info['filename'], 'r').readlines():
if 'indexedmzML' in line:
# writing of indexed mzML is not possible at the moment
continue
if 'run' in line:
# the run is appended from the original parser to avoid messing
# with the new xml tree, we break before the run data starts
break
input_xml_string += line
if 'softwareList' in line and pymzml_tag_written is False:
addon = cElementTree.Element(
'software',
{
'id' : 'pymzML',
'version' : "0.7.6"
}
)
cElementTree.SubElement(
addon,
'cvParam',
{
'accession' : 'MS:1000531',
'cvRef' : 'MS',
'name' : 'pymzML Writer',
'version' : '0.7.6',
}
)
new_line = cElementTree.tostring(addon, encoding='utf-8')
input_xml_string += new_line
pymzml_tag_written = True
input_xml_string += '</mzML>\n'
self.newTree = cElementTree.fromstring(input_xml_string)
for event, element in cElementTree.iterparse(io, events=(b'start', b'end')):
if event ==b'start':
if element.tag.endswith('}run'):
self.lookup['run'] = cElementTree.Element(element.tag, element.attrib)
if element.tag.endswith('}spectrumList'):
self.lookup['spectrumList'] = \
cElementTree.Element(element.tag, element.attrib)
self.lookup['spectrumIndeces'] = \
cElementTree.Element('index', {'name': 'spectrum'})
break
return
def __init__(self):
HTMLParser.__init__(self)
self.tb = etree.TreeBuilder()
def __str__(self):
"""Return string representation"""
builder = ET.TreeBuilder()
self.build(builder)
return ET.tostring(builder.close(), encoding='utf-8').decode('utf-8')
def unflatten(tree):
builder = cElementTree.TreeBuilder()
if not tree:
return ''
tag = None
root_element = None
paths = []
for row in tree:
current_path = []
data = ''
create_new_element = True
for column in row:
if column[0] == '!':
create_new_element = False
data = column[1:]
else:
current_path.append(column)
tags_to_end = []
last_path = paths[-1] if paths else []
if not data and current_path == last_path:
tags_to_end.append(tag)
for i, a in enumerate(last_path):
tag_to_end = None
if i >= len(current_path):
tag_to_end = a
else:
b = current_path[i]
if a != b:
tag_to_end = a
if tag_to_end:
tags_to_end.append(tag_to_end)
for tag_to_end in tags_to_end[::-1]:
builder.end(tag_to_end)
paths.pop()
last_path = paths[-1] if paths else []
if not data and current_path == last_path:
builder.end(tag_to_end)
paths.pop()
tag = current_path[-1]
if create_new_element:
builder.start(tag)
if data:
builder.data(data)
paths.append(current_path)
builder.end(tag)
root_element = builder.close()
if root_element is None:
return ''
return cElementTree.tostring(root_element)
def __init__(self, partial=False, _parsetree_roundtrip=False): self.partial = partial self._b = ElementTreeModule.TreeBuilder() self.stack = [] #: keeps track of current open elements self._last_char = None self._parsetree_roundtrip = _parsetree_roundtrip
def __init__(self):
HTMLParser.HTMLParser.__init__(self)
self.tree_builder = ElementTree.TreeBuilder()
self.tree = None
def __init__(self, encoding=None):
_HTMLParser.__init__(self)
self._target = ElementTree.TreeBuilder()
def getroot(self):
"""Build XML object, return the root"""
builder = ET.TreeBuilder()
self.build(builder)
return builder.close()
