def fetchData():
global wd
wd = str(os.getcwd())
print('All Files will go into the celpp folder')
cred = (wd + '/credentials.txt')
try: #attempts to connect to file required to connect to ftp
print('Trying to open credentials.txt')
fo = open(cred, 'r')
fo.close()
except: #writes file required to connect to ftp if not already made
print('Writing credentials.txt file')
fo = open(cred, 'w')
fo.write(
'host ftp.box.com\nuser [email protected]\npass #hail2pitt1\npath\ncontestantid 33824\nchallengepath /challengedata\nsubmissionpath /33824'
)
fo.close()
if (os.path.isdir(wd + '/challengedata') == False
): #creates challengedata folder if it doesn't exist
os.mkdir(wd + '/challengedata')
os.chdir(wd + '/challengedata')
else: #changes to challengedata folder if it exists
os.chdir(wd + '/challengedata')
ftp = FtpFileTransfer(cred)
print('Connecting to ftp.box.com')
ftp.connect()
print('Connected to ftp')
ftp_files = ftp.list_files(
'challengedata') #creates list of files from box
count = 0 #keep track number of files added to local folder
for x in (ftp_files):
split = os.path.splitext(x)
dir = os.path.splitext(split[0])
if (str(split[1]) == '.gz'):
if os.path.isfile(
x
) == True: #if it finds the zip file in local folder, unzips and deletes zippped file
print('Unzipping folder ' + str(dir[0]))
os.system('tar -xzf ' + x)
print('Deleting zip file: ' + x)
os.system('rm ' + x)
elif os.path.isdir(
str(dir[0])
) == True: #if it finds the unzipped directory in local folders
pass
else: #if it can't find the week in any format; downloads, unzips, and removes zipped file
ftp.download_file('challengedata/' + x,
wd + '/challengedata/' + x)
print('Unzipping folder ' + str(dir[0]))
os.system('tar -xzf ' + x)
print('Deleting zip file: ' + x)
os.system('rm ' + x)
count = count + 1
print(
str(dir[0]) +
' was just added to the challengedata folder')
else:
ftp.download_file('challengedata/' + x,
wd + '/challengedata/' + x)
print('challengedata has been updated. ' + str(count) +
' week(s) was/were just added.')
print('Disconnecting from ftp')
ftp.disconnect()
def fetch_visual_file():
global wd
wd = str(os.getcwd())
print('All Files will go into the celpp folder')
cred = (wd + '/credentials.txt')
try: #attempts to connect to file required to connect to ftp
print('Trying to open credentials.txt')
fo = open(cred, 'r')
fo.close()
except: #writes file required to connect to ftp if not already made
print('Writing credentials.txt file')
fo = open(cred, 'w')
fo.write('host ftp.box.com\nuser [email protected]\npass #hail2pitt1\npath\ncontestantid 33824\nchallengepath /challengedata\nsubmissionpath /33824')
fo.close()
if(os.path.isdir(wd + '/challengedata_Visualizaiton')==False):#creates challengedata folder if it doesn't exist
print('challengedata_Visualizaiton directory does not exists. ')
os.mkdir(wd + '/challengedata_Visualizaiton')
os.chdir(wd + '/challengedata_Visualizaiton')
else: #changes to challengedata folder if it exists
os.chdir(wd + '/challengedata_Visualizaiton')
ftp = FtpFileTransfer(cred)
print('Connecting to ftp.box.com')
ftp.connect()
print('Connected to ftp')
ftp_files = ftp.list_files('challengedata')#creates list of files from box
for x in (ftp_files):
if (x == 'visual.txt'):
ftp.download_file('challengedata/' + x, wd + '/challengedata/' + x)
ftp.disconnect()
print('Disconnected from ftp')
def box_plot(rmsd, week_num):
x_data = list(rmsd.keys())
y_data = []
for x in x_data:
data = rmsd.get(x)
y_data.append(data)
y_best_rmsd = []
y_first_rmsd = []
for y in y_data:
min_rmsd = min(y)
first_rmsd = y[0]
y_best_rmsd.append(min_rmsd)
y_first_rmsd.append(first_rmsd)
N = len(x_data)
colors = ['hsl('+str(h)+',50%'+',50%)' for h in np.linspace(0, 360, N)]
traces = []
for xd, yd, ybest, yfirst, cls in zip(x_data, y_data, y_best_rmsd, y_first_rmsd, colors):
traces.append(go.Box(
y=yd,
name=xd,
boxpoints='all',
jitter=1,
whiskerwidth=1,
pointpos = -2,
fillcolor=cls,
marker=dict(size=3,),
line=dict(width=1.5),))
traces.append(go.Scatter(
showlegend = True,
legendgroup = 'Best RMSD',
y = ybest,
x = xd,
name = xd + ' Best RMSD',
fillcolor=cls,
marker = dict(size = 15, symbol = 'square-open', ), ))
traces.append(go.Scatter(
showlegend = True,
legendgroup = 'First Pose RMSD',
y = yfirst,
x = xd,
name = xd + ' First Pose RMSD',
fillcolor = cls,
marker = dict(size = 15, symbol = 'star', ),))
layout = go.Layout(title='RMSD for all Targets in Week' + str(week_num),
yaxis=dict(autorange=True,showgrid=True,zeroline=True,dtick=5,
gridcolor='rgb(255, 255, 255)', gridwidth=1,
zerolinecolor='rgb(255, 255, 255)',zerolinewidth=2,),
margin=dict(l=40,r=30,b=80,t=100,),
paper_bgcolor='rgb(243, 243, 243)',
plot_bgcolor='rgb(243, 243, 243)',
showlegend=False)
fig = go.Figure(data=traces, layout=layout)
return fig
def bar_plot(rmsd, week_num):
x_data = list(rmsd.keys())
y_data = []
for x in x_data:
data = rmsd.get(x)
y_data.append(data)
y_best_rmsd = []
y_first_rmsd = []
for y in y_data:
min_rmsd = min(y)
first_rmsd = y[0]
y_best_rmsd.append(min_rmsd)
y_first_rmsd.append(first_rmsd)
trace1 = go.Bar(
x = x_data,
y = y_best_rmsd,
name='Best RMSD'
)
trace2 = go.Bar(
x = x_data,
y = y_first_rmsd,
name='First Pose RMSD'
)
data = [trace1, trace2]
layout = go.Layout(title='Best and First Pose RMSD for all Targets in Week' + str(week_num),
barmode='group'
)
fig = go.Figure(data=data, layout=layout)
return fig
def uploadData(
): #uploads zip files containing docking predictions to contestant folder specified in credentials.txt
print('Uploading files to box contestant folder')
cred = wd + '/credentials.txt'
ftp = FtpFileTransfer(cred)
print('Connecting to ftp.box.com')
ftp.connect()
print('Connected to ftp')
ftp_files = ftp.list_files(
ftp.get_contestant_id()) #creates list of files from box
d = []
for (_, dirnames, _) in os.walk(wd + '/protocols'):
d.extend(dirnames)
break
for dir in (
d
): #NOT A FAN OF THE NESTED FOR LOOPS, WILL TRY TO FIND BETTER WAY TO IMPLEMENT THIS
for (_, _, filenames) in os.walk(wd + '/protocols/' + dir):
f = []
f.extend(filenames)
print('Uploading files for ' + dir)
for x in (f):
if ((x in ftp_files) == False):
file = wd + '/protocols/' + dir + '/' + x
remote_dir = ftp.get_remote_submission_dir()
remote_file_name = os.path.basename(file)
ftp.upload_file_direct(file, remote_dir,
remote_file_name)
else:
pass
print('All the files have been uploaded. Disconnecting from ftp')
ftp.disconnect()