def test_check_with_missing_yaml_terminator():
header = """
---
layout: workshop
root: .
<!--
Edit the values in the block above to be appropriate for your
workshop. Run 'tools/check' *before* committing to make sure that
changes are good.
-->
"""
assert check.check_file('test.html', header) != []
def test_check_with_missing_yaml_terminator():
header = """
---
layout: workshop
root: .
<!--
Edit the values in the block above to be appropriate for your
workshop. Run 'tools/check' *before* committing to make sure that
changes are good.
-->
"""
assert check.check_file('test.html', header) != []
def test_check_without_enddate():
header = """---
layout: workshop
root: .
venue: Euphoric State University
address: 123 College Street, Euphoria
country: United-States
humandate: Feb 17-18, 2020
humantime: 9:00 am - 4:30 pm
startdate: 2020-06-17
latlng: 41.7901128,-87.6007318
instructor: ["Grace Hopper", "Alan Turing"]
contact: [email protected]
helper: [ "John von Neumann" ]
---"""
assert check.check_file('test.html', header) == []
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-l",
"--path_to_links",
dest="links_path",
help="text file having list of download links",
type=str,
required=True)
parser.add_argument("-d",
"--destination",
dest="download_directory",
help="download location of files",
type=str,
required=True)
parser.add_argument("-u",
"--username",
dest="username",
help="username for website",
type=str,
required=True)
parser.add_argument("-p",
"--password",
dest="password",
help="password for website",
type=str,
required=True)
parser.add_argument("-n",
"--threads",
dest="thread_count",
help="amount of threads for download",
type=int,
required=True)
args = parser.parse_args()
file = check.check_file(args.links_path)
directory = check.check_dir(args.download_directory)
start = time.time()
ThreadedFunction.RunMethodWithThreads(
LinkDownload.link_download,
(file, directory, args.username, args.password), args.thread_count)
end = time.time()
elapsed_time = end - start
print("\n -- Total Download Time: %d:%.2d --\n" %
(elapsed_time / 60, elapsed_time % 60))
return 0
def test_check_without_enddate():
header = """---
layout: workshop
root: .
venue: Euphoric State University
address: 123 College Street, Euphoria
country: United-States
humandate: Feb 17-18, 2020
humantime: 9:00 am - 4:30 pm
startdate: 2020-06-17
latlng: 41.7901128,-87.6007318
instructor: ["Grace Hopper", "Alan Turing"]
contact: [email protected]
helper: [ "John von Neumann" ]
---"""
assert check.check_file('test.html', header) == []
def test_check_with_enddate():
header_sample = """---
layout: workshop
root: .
venue: Euphoric State University
address: 123 College Street, Euphoria
country: United-States
humandate: Feb 17-18, 2020
humantime: 9:00 am - 4:30 pm
startdate: 2020-06-17
enddate: 2020-06-18
latlng: 41.7901128,-87.6007318
instructor: ["Grace Hopper", "Alan Turing"]
helper: [ ]
contact: [email protected]
---"""
assert check.check_file(make_file(header_sample))
def __get_pdb_box(pdb_file_path):
"""
计算蛋白或者配体的空间中心坐标和最大立方体长宽高。
:param pdb_file_path: pdb或者pdbqt文件路径名
:return: 中心x坐标，中心y坐标，中心z坐标，长，宽，高。
"""
# 保证文件存在
if not check.check_file(pdb_file_path):
print(pdb_file_path + "不存在")
sys.exit()
atoms_x_list = []
atoms_y_list = []
atoms_z_list = []
# 额外距离
extra_distance = 0
# 读取所有非H原子的坐标
with open(pdb_file_path, encoding='UTF-8') as f:
lines = f.readlines()
for line in lines:
if line.startswith("ATOM") or line.startswith("HETATM"):
if line[13:14] != "H":
atoms_x_list.append(float(line[30:38]))
atoms_y_list.append(float(line[38:46]))
atoms_z_list.append(float(line[46:54]))
if len(atoms_x_list) == 0:
print("没有检测到原子")
sys.exit()
box_center_x = round(sum(atoms_x_list) / len(atoms_x_list), 3)
box_center_y = round(sum(atoms_y_list) / len(atoms_y_list), 3)
box_center_z = round(sum(atoms_z_list) / len(atoms_z_list), 3)
box_length = round(max(atoms_x_list) - min(atoms_x_list),
1) + extra_distance
box_width = round(max(atoms_y_list) - min(atoms_y_list),
1) + extra_distance
box_height = round(max(atoms_z_list) - min(atoms_z_list),
1) + extra_distance
return box_center_x, box_center_y, box_center_z, box_length, box_width, box_height
def test_check_with_leading_blank_lines():
header = """
---
layout: workshop
root: .
venue: Euphoric State University
address: 123 College Street, Euphoria
country: United-States
humandate: Feb 17-18, 2020
humantime: 9:00 am - 4:30 pm
startdate: 2020-06-17
enddate: 2020-06-18
latlng: 41.7901128,-87.6007318
instructor: ["Grace Hopper", "Alan Turing"]
helper: [ ]
contact: [email protected]
eventbrite: # FIXME
---"""
assert check.check_file('test.html', header) != []
def test_check_with_leading_blank_lines():
header = """
---
layout: workshop
root: .
venue: Euphoric State University
address: 123 College Street, Euphoria
country: United-States
humandate: Feb 17-18, 2020
humantime: 9:00 am - 4:30 pm
startdate: 2020-06-17
enddate: 2020-06-18
latlng: 41.7901128,-87.6007318
instructor: ["Grace Hopper", "Alan Turing"]
helper: [ ]
contact: [email protected]
eventbrite: # FIXME
---"""
assert check.check_file('test.html', header) != []
def upload_file():
global prev
files = request.files.getlist('files[]')
WL1 = request.form.get("WL1")
WL2 = request.form.get("WL2")
for file in files:
if file:
if allowed_file(file.filename):
filename = time.strftime("%Y%m%d-%H%M%S")
filename += "_unprocessed_" + "WL1_" + WL1 + "_WL2_" + WL2 + ".csv"
file.save(os.path.join(app.config['UPLOAD_FOLDER'], filename))
if not check_file(filename):
flash("Improper format")
os.remove(
os.path.join(app.config['UPLOAD_FOLDER'], filename))
else:
update_file(filename)
else:
flash('File extension not supported!')
prev = filename
return redirect('/')
#!/usr/bin/python3
from check import check_file
from utils import *
cdname = os.path.dirname(__file__)
archive_folder = os.path.join(cdname, 'archive', '201711')
if __name__ == '__main__':
for root, dirs, files in os.walk(archive_folder):
for file in sorted(files):
check_file(os.path.join(root, file))
#!/usr/bin/python3
import os
from check import check_file, max_missed_pid
from utils import my_log
cdname = os.path.dirname(__file__)
archive_dir = os.path.join(cdname, 'archive', '201810')
if __name__ == '__main__':
last_pid = None
for root, dirs, files in os.walk(archive_dir):
for file in sorted(files):
filename = os.path.join(root, file)
oldest_pid, newest_pid = check_file(filename)
# Check missed posts between files
if oldest_pid:
if (last_pid and oldest_pid > last_pid + 1
and oldest_pid < last_pid + max_missed_pid):
for i in range(last_pid + 1, oldest_pid):
my_log('{} {} MISSED BETWEEN FILES'.format(i, file))
last_pid = oldest_pid
