def load_from_file(path):
path = osp.expanduser(path)
if osp.exists(osp.dirname(path)):
dict_imp = DictImporter(nodecls=DPNode)
imp = JsonImporter(dictimporter=dict_imp,
object_hook=tools.object_hook)
with open(path, "r") as f:
res = imp.read(f)
return RemoteTree(res)
else:
print("Error saving to disk. Dir {} not existing.".format(
osp.dirname(path)))
import sys
from anytree.importer import JsonImporter
from anytree import *
if __name__ == '__main__':
filename = sys.argv[1]
importer = JsonImporter()
with open(filename) as filehandle:
tree = importer.read(filehandle)
print(filename + ' Tree', end='\n\n')
print(RenderTree(tree))
import json # Base library
from xml.dom import minidom
from anytree import RenderTree # pip3 install anytree
from anytree.importer import DictImporter
from anytree.importer import JsonImporter
from sbomify.sbomlibrary import SbomLibrary
tree = {}
with open("out.json", "r") as f:
baseimporter = DictImporter(nodecls=SbomLibrary)
importer = JsonImporter(dictimporter=baseimporter)
tree = importer.read(f)
tree
# print(RenderTree(tree))
thestr = tree.toSWID()
print(thestr)
# reparsed = minidom.parseString(thestr)
# print(reparsed.toprettyxml(indent=" "))
m = main_xml.find('processTree')
for e in content_to_copy.find('processTree'):
m.append(e)
def changing_id(xml, needle, replace_by):
for e in xml.find('processTree'):
for a in ['id', 'sourceId', 'targetId']:
if a in e.attrib.keys():
if e.attrib[a] == needle:
e.attrib[a] = replace_by
importer = JsonImporter()
with open('1_split/rendertree.json', 'r') as f:
root = importer.read(f)
main = ET.parse('2_gather/{}.ptml'.format(root.name))
print(RenderTree(root))
for c in root.children:
sub = ET.parse('2_gather/{}.ptml'.format(c.name))
id_in_main = get_by_name(main, c.name).attrib['id']
id_in_sub = sub.find('processTree').attrib['root']
delete_node(main, id_in_main)
changing_id(sub, id_in_sub, id_in_main)
add_content(main, sub)
main.write('2_gather/pt.ptml')
def _deserialize_ontology(filename): """Deserializes an ontology from a JSON file and returns its root.""" importer = JsonImporter() return importer.read(filename)
def main():
parser = get_args()
if not sys.argv[1:]:
sys.exit(parser.print_help())
#Load args
args = parser.parse_args()
n = 0
importer = JsonImporter()
with open(args.three_prime_template_file) as json_data:
three_prime_template = importer.read(json_data)
with open(args.five_prime_template_file) as json_data:
five_prime_template = importer.read(json_data)
hairpins_list=set()
reference = defaultdict()
with open(args.hairpin_path, 'rt') as hairpins, open(args.mature_path, 'rt') as mature:
#Load hairpins ref
all_lines = hairpins.read()
hairpins = all_lines.split('>')
del hairpins[0]
for line in hairpins:
line = line.split('\n',1)
hairpins_list.add(line[1].replace('\n',''))
#Load mature RNA
for line in mature:
line2 = next(mature).strip()
name = line.strip()
if line2 in reference:
reference[line2]['name'] = '{}={}'.format(reference[line2]['name'],name.lstrip('>'))
else:
reference[line2]=defaultdict()
reference[line2]['name'] = name
reference[line2]['5_prime_tree'] = copy.deepcopy(five_prime_template)
reference[line2]['3_prime_tree'] = copy.deepcopy(three_prime_template)
num_seqs = len(reference.keys())
widgets = [progressbar.Percentage(), progressbar.Bar()]
print('Mapping isomir modifications to reference.')
count=0
bar = progressbar.ProgressBar(widgets=widgets, max_value=num_seqs).start()
for sequence in reference.keys():
match_one_end(sequence=sequence,reference_dict=reference[sequence],end=5,hairpin_reference=hairpins_list)
match_one_end(sequence=sequence,reference_dict=reference[sequence],end=3,hairpin_reference=hairpins_list)
count+=1
bar.update(count)
print()
print('Generating new reference.')
count = 0
new_reference = defaultdict()
bar = progressbar.ProgressBar(widgets=widgets, max_value=num_seqs).start()
for sequence in reference.keys():
new_reference = generate_string_general(sequence, reference, new_reference)
count+=1
bar.update(count)
print()
print('Checking for multireads.')
with open(args.out_path,'w') as out_file:
with open(args.multireads_path,'w') as multireads_out:
for sequence in new_reference:
if(len(new_reference[sequence])>1):
ordered_names = order_multireads(names=new_reference[sequence])
multireads_out.write('{}\n{}\n\n'.format('\n'.join(ordered_names), sequence))
out_file.write('{}_multi\n{}\n'.format(ordered_names[0],sequence))
else:
out_file.write('{}_unique\n{}\n'.format(next(iter(new_reference[sequence])),sequence))
print('Isomir reference created.')
def analyze(self):
"""Do everything."""
def reset_display():
# Reset display
self.suffix = "?JSTool=none"
self.script_buttons.clear()
self.choice_boxes.clear()
self.number_of_buttons = 0
# self.diff_btn.Show()
self.apply_btn.Show()
self.save_btn.Show()
self.content_panel.Show()
self.content_text.SetValue("Script code")
while self.script_sizer.GetChildren():
self.script_sizer.Hide(0)
self.script_sizer.Remove(0)
self.images.clear()
def get_index_html():
# Get index.html from remote proxy
return get_resource(self.url)
def parse_html(html: str):
# Add index.html scripts to self.script_tree
cnt = 1
if not html:
return
while "<script" in html:
src = ""
script_name = "script" + str(cnt)
start_index = html.find("<script")
end_index = html.find("</script>")
text = html[start_index:end_index + 9]
new_node = AnyNode(id=script_name,
parent=self.script_tree,
content=text,
vector=extract_features(text),
count=1)
if ' src="' in text: # BeautifulSoup turns all single quotes into double quotes
src = text.split(' src="')[1].split('"')[0]
src = self.format_src(src)
try:
node = anytree.cachedsearch.find(
self.script_tree, lambda node: node.id == src)
except anytree.search.CountError:
logging.warning(
'multiple possible parents: more than one node with id = %s',
src)
if node:
node.parent = new_node
html = html.replace(text, "\n<!--" + script_name + "-->\n")
cnt += 1
def create_buttons():
# Add checkboxes to display
# Check all
self.add_button('Check all', 0, 1, None)
index = 1
# All other script checkboxes
for node in PreOrderIter(self.script_tree):
if node.is_root:
continue
node.button = index
# vector = extract_features(node.content)
self.add_button(node.id, index, node.depth,
get_attribute(node, 'vector')) # node.count
checkbox = self.script_buttons[index]
if (get_attribute(checkbox, 'confidence') is not None
and get_attribute(
checkbox, 'confidence') < CONFIDENCE_THRESHOLD):
# run clustering if confidence less than threshold
checkbox.category = CLUSTER.predict(script=str(
node.content),
preprocess=True)
label = get_attribute(checkbox, 'label')
if label:
label.SetLabel(checkbox.category)
label.SetBackgroundColour(
tuple(CATEGORIES[checkbox.category]['color']))
label.SetToolTip(
CATEGORIES[checkbox.category]['description'])
if get_attribute(checkbox,
'category') not in BLOCKED_CATEGORIES:
# ads / marketing scripts disabled by default
try:
if node.id[:6] != "script":
self.blocked_urls.remove(node.id)
except ValueError:
logging.debug("Could not remove %s from blocked urls",
node.id)
self.check_boxes(True, node)
index += 1
self.scripts_panel.SetSizer(self.script_sizer)
self.frame.frame_sizer.Layout()
def functional_dependency():
# functional dependencies?
try:
tmp_dep = perf.get_dependency(self.url)
# tmp_dep = [['https://ws.sharethis.com/button/async-buttons.js', 'https://www.google-analytics.com/analytics.js', 'https://ws.sharethis.com/button/buttons.js'], ['https://www.googletagmanager.com/gtm.js?id=GTM-WBDQQ5', 'https://www.googleadservices.com/pagead/conversion_async.js'], ['https://www.unicef.org/sites/default/files/js/js_B7pS3ddmNLFYOJi3j28odiodelMu-EhaOeKlHZ8E6y0.js', 'https://www.unicef.org/themes/custom/unicef/assets/src/js/init-blazy.js?v=1.x', 'https://www.unicef.org/sites/default/files/js/js_dWWS6YNlsZWmXLboSy3PIiSD_Yg3sRxwjbMb52mdNyw.js', 'https://www.unicef.org/sites/default/files/js/js_cLlwgRdoiVfjtFxLqlXX-aVbv3xxfX_uMCsn7iJqNpA.js']]
print("\n\n-------- DEPENDENCY LABELS CHANGED --------")
mapping = {'non-critical': 0, 'translatable': 1, 'critical': 2}
mapping2 = {
0: 'non-critical',
1: 'translatable',
2: 'critical'
}
for a in tmp_dep:
tmp_label = 0
for i in a:
if i not in self.yasir or self.yasir[
i].category not in mapping:
continue
if mapping[self.yasir[i].category] > tmp_label:
tmp_label = mapping[self.yasir[i].category]
for i in a:
if i not in self.yasir or self.yasir[
i].category not in mapping:
continue
if self.yasir[i].category != mapping2[tmp_label]:
print("****", i, mapping2[tmp_label],
self.yasir[i].category)
print("\n\n")
except RuntimeError:
pass
def display_loading_message():
# Never managed to get this part to display before spinning wheel of death
self.err_msg.SetForegroundColour((0, 0, 0))
self.err_msg.SetLabel("Loading page... please wait")
self.Update()
def similarity():
# Print script pairs in self.script_tree with Jaccard similarity > SIMILARITY_THRESHOLD
names = []
scripts = []
for node in PreOrderIter(self.script_tree):
if node.is_root:
continue
names.append(node.id)
scripts.append(str(node.content))
results = similarity_comparison(scripts, SIMILARITY_THRESHOLD)
if results:
print("---" * 20)
print('scripts with similarity > %.2f' % SIMILARITY_THRESHOLD)
for tup in results:
print('%s %s %.2f' % (names[tup[0]], names[tup[1]], tup[2]))
def compare_image_sizes(images):
# Print difference in original and rendered image sizes for image URLs in images
for url in images:
if url[:4] == 'data':
# URI rather than URL
url = url.partition(';')[-1]
body = url.partition(',')[-1]
if url[:6] == 'base64':
body = base64.b64decode(body)
else:
body = get_resource(url)
try:
stream = BytesIO(body)
except TypeError:
logging.warning("body in %s, not in bytes", type(body))
stream = BytesIO(body.encode(ENCODING))
try:
width, height = get_image_size_from_bytesio(
stream, DEFAULT_BUFFER_SIZE)
self.images[url] = {}
self.images[url]['ow'] = width
self.images[url]['oh'] = height
except UnknownImageFormat as error:
logging.exception(str(error))
except struct.error as error:
logging.error(str(error))
for img in self.driver.find_elements_by_tag_name('img'):
url = img.get_attribute('src')
if url not in self.images.keys():
self.images[url] = {}
self.images[url]['rw'] = img.size['width']
self.images[url]['rh'] = img.size['height']
logging.info("---" * 20)
logging.info("potential image improvements:")
for url, dimensions in self.images.items():
if len(dimensions.keys()) == 4:
# Successfully parsed original and rendered dimensions
logging.info(url)
logging.info("original: %d x %d", dimensions['ow'],
dimensions['oh'])
logging.info("rendered: %d x %d", dimensions['rw'],
dimensions['rh'])
display_loading_message()
# Reset values
self.url = self.url_input.GetValue()
if self.url[-1] != "/":
self.url = self.url + "/"
if not self.url:
return
reset_display()
self.script_tree = AnyNode(id=self.url)
try:
file_path = PATH + "/reports/" + self.url.split("/")[2]
if not os.path.exists(file_path):
os.mkdir(file_path)
with open(file_path + "/script_tree.txt", 'r') as f:
logging.debug('importing script tree...')
importer = JsonImporter()
self.script_tree = importer.read(f)
with open(file_path + "/images.json", 'r') as f:
images = json.load(f)
except FileNotFoundError:
logging.debug('script tree does not yet exist, building now')
# Get original page and parse external scripts
self.driver.execute_cdp_cmd('Network.setBlockedURLs', {'urls': []})
epoch_in_milliseconds = time.time() * 1000
try:
self.driver.get(self.url)
self.err_msg.SetLabel("")
except InvalidArgumentException as exception:
self.err_msg.SetForegroundColour((255, 0, 0)) # make text red
self.err_msg.SetLabel(str(exception))
return
self.wait_for_load()
self.script_tree = AnyNode(id=self.url)
scripts, images = self.parse_log(epoch_in_milliseconds)
for script in scripts:
# pylint: disable=undefined-loop-variable
# pylint: disable=cell-var-from-loop
parent = anytree.cachedsearch.find(
self.script_tree,
lambda node: node.id == self.format_src(script['parent']))
# Check if this node already exists
node = anytree.cachedsearch.find(
self.script_tree,
lambda node: node.id == self.format_src(script['url']))
if node and node.parent == parent:
logging.warning('duplicate script! %s',
self.format_src(script['url']))
node.count += 1
else:
AnyNode(id=self.format_src(script['url']),
parent=parent,
content=script['content'],
vector=extract_features(script['content']),
count=1)
# Check image differences
compare_image_sizes(images)
# Parse inline scripts
html = get_index_html()
parse_html(html)
# self.print_scripts()
# Export script tree
logging.debug('exporting script tree...')
exporter = JsonExporter()
with open(
PATH + "/reports/" + self.url.split("/")[2] +
"/script_tree.json", "w") as f:
exporter.write(self.script_tree, f)
logging.debug('done')
# Export images
with open(
PATH + "/reports/" + self.url.split("/")[2] +
"/images.json", "w") as f:
json.dump(images, f)
# Check similarity
# similarity()
# Create buttons
self.block_all_scripts()
create_buttons()
# Print functional dependencies
# functional_dependency()
# Get page with all scripts removed
self.on_apply_press()
try:
self.original.get(self.url)
except InvalidArgumentException as e:
logging.error(e.what())