def processInputData(request):
'''
Extract File name & determine what file corresponds to what for gengraph
@param request: the request object
'''
filesInUploadDir = os.listdir(request.session['derivatives'])
roi_xml_fn, fiber_fn, roi_raw_fn = filesorter.checkFileExtGengraph(filesInUploadDir) # Check & sort files
for fileName in [roi_xml_fn, fiber_fn, roi_raw_fn]:
if fileName == "": # Means a file is missing from i/p
return render_to_response('pipelineUpload.html', context_instance=RequestContext(request)) # Missing file for processing Gengraph
baseName = fiber_fn[:-9] # MAY HAVE TO CHANGE
''' Fully qualify file names '''
fiber_fn = os.path.join(request.session['derivatives'], fiber_fn)
roi_raw_fn = os.path.join(request.session['derivatives'], roi_raw_fn)
roi_xml_fn = os.path.join(request.session['derivatives'], roi_xml_fn)
try:
request.session['smGrfn'], request.session['bgGrfn'], request.session['lccfn']\
,request.session['SVDfn'] = processData(fiber_fn, roi_xml_fn, roi_raw_fn, \
request.session['graphs'], request.session['graphInvariants'],\
request.session['graphsize'], True)
except:
if request.session['graphsize'] == 'big':
msg = "Hello,\n\nYour most recent job failed either because your fiber streamline file or ROI mask was incorrectly formatted."
msg += " Please check both and try again.%s\n\n" % (" "*randint(0,10))
sendJobFailureEmail(request.session['email'], msg)
return HttpResponseRedirect(get_script_prefix()+"jobfailure")
# Run ivariants here
if len(request.session['invariants']) > 0:
print "Computing invariants"
if (request.session['graphsize'] == 'big'):
graph_fn = request.session['bgGrfn']
lcc_fn = request.session['lccfn']
elif (request.session['graphsize'] == 'small'):
graph_fn = request.session['smGrfn']
lcc_fn = None
request.session['invariant_fns'] = runInvariants(request.session['invariants'],\
graph_fn, request.session['graphInvariants'],\
lcc_fn, request.session['graphsize'])
if request.session['graphsize'] == 'big':
sendJobCompleteEmail(request.session['email'], 'http://mrbrain.cs.jhu.edu' + request.session['usrDefProjDir'].replace(' ','%20'))
return HttpResponseRedirect(get_script_prefix()+'confirmdownload')
def processInputData(request):
'''
Extract File name & determine what file corresponds to what for gengraph
@param request: the request object
'''
filesInUploadDir = os.listdir(request.session['derivatives'])
roi_xml_fn, fiber_fn, roi_raw_fn = filesorter.checkFileExtGengraph(
filesInUploadDir) # Check & sort files
for fileName in [roi_xml_fn, fiber_fn, roi_raw_fn]:
if fileName == "": # Means a file is missing from i/p
return render_to_response(
'pipelineUpload.html',
context_instance=RequestContext(
request)) # Missing file for processing Gengraph
baseName = fiber_fn[:-9] # MAY HAVE TO CHANGE
''' Fully qualify file names '''
fiber_fn = os.path.join(request.session['derivatives'], fiber_fn)
roi_raw_fn = os.path.join(request.session['derivatives'], roi_raw_fn)
roi_xml_fn = os.path.join(request.session['derivatives'], roi_xml_fn)
request.session['smGrfn'], request.session['bgGrfn'], request.session['lccfn']\
,request.session['SVDfn'] = processData(fiber_fn, roi_xml_fn, roi_raw_fn, \
request.session['graphs'], request.session['graphInvariants'],\
request.session['graphsize'], True)
# Run ivariants here
if len(request.session['invariants']) > 0:
print "Computing invariants"
if (request.session['graphsize'] == 'big'):
graph_fn = request.session['bgGrfn']
lcc_fn = request.session['lccfn']
elif (request.session['graphsize'] == 'small'):
graph_fn = request.session['smGrfn']
lcc_fn = None
request.session['invariant_fns'] = runInvariants(request.session['invariants'],\
graph_fn, request.session['graphInvariants'],\
lcc_fn, request.session['graphsize'])
return HttpResponseRedirect(get_script_prefix() + 'confirmdownload')
def processInputData(request):
'''
Extract File name & determine what file corresponds to what for gengraph
@param request: the request object
'''
filesInUploadDir = os.listdir(request.session['derivatives'])
roi_xml_fn, fiber_fn, roi_raw_fn = filesorter.checkFileExtGengraph(filesInUploadDir) # Check & sort files
for fileName in [roi_xml_fn, fiber_fn, roi_raw_fn]:
if fileName == "": # Means a file is missing from i/p
return render_to_response('pipelineUpload.html', context_instance=RequestContext(request)) # Missing file for processing Gengraph
baseName = fiber_fn[:-9] # MAY HAVE TO CHANGE
''' Fully qualify file names '''
fiber_fn = os.path.join(request.session['derivatives'], fiber_fn)
roi_raw_fn = os.path.join(request.session['derivatives'], roi_raw_fn)
roi_xml_fn = os.path.join(request.session['derivatives'], roi_xml_fn)
request.session['smGrfn'], request.session['bgGrfn'], request.session['lccfn']\
,request.session['SVDfn'] = processData(fiber_fn, roi_xml_fn, roi_raw_fn, \
request.session['graphs'], request.session['graphInvariants'],\
request.session['graphsize'], True)
# Run ivariants here
if len(request.session['invariants']) > 0:
print "Computing invariants"
if (request.session['graphsize'] == 'big'):
graph_fn = request.session['bgGrfn']
lcc_fn = request.session['lccfn']
elif (request.session['graphsize'] == 'small'):
graph_fn = request.session['smGrfn']
lcc_fn = None
request.session['invariant_fns'] = runInvariants(request.session['invariants'],\
graph_fn, request.session['graphInvariants'],\
lcc_fn, request.session['graphsize'])
return HttpResponseRedirect(get_script_prefix()+'confirmdownload')
def upload(request, webargs=None):
"""
Programmatic interface for uploading data
@param request: the request object
@param webargs: POST data with userDefProjectName, site, subject, session, scanId, graphsize, [list of invariants to compute] info
"""
# request.session.clear()
if (webargs and request.method == 'POST'):
# Check for malformatted input
webargs = webargs[1:] if webargs.startswith('/') else webargs
webargs = webargs[:-1] if webargs.endswith('/') else webargs
if len(webargs.split('/')) == 7:
[
userDefProjectName, site, subject, session, scanId, graphsize,
request.session['invariants']
] = webargs.split('/')
request.session['invariants'] = request.session[
'invariants'].split(',')
elif len(webargs.split('/')) == 6:
[userDefProjectName, site, subject, session, scanId,
graphsize] = webargs.split('/')
userDefProjectDir = adaptProjNameIfReq(
os.path.join(settings.MEDIA_ROOT, 'public', userDefProjectName,
site, subject, session, scanId))
''' Define data directory paths '''
derivatives, rawdata, graphs, request.session[
'graphInvariants'], images = defDataDirs(userDefProjectDir)
''' Make appropriate dirs if they dont already exist '''
createDirStruct.createDirStruct([
derivatives, rawdata, graphs, request.session['graphInvariants'],
images
])
print 'Directory structure created...'
uploadFiles = writeBodyToDisk(request.body, derivatives)
# Check which file is which
roi_xml_fn, fiber_fn, roi_raw_fn = filesorter.checkFileExtGengraph(
uploadFiles) # Check & sort files
''' Data Processing '''
if (re.match(re.compile('(b|big)', re.IGNORECASE), graphsize)):
request.session['graphsize'] = 'big'
request.session['smGrfn'], request.session['bgGrfn'], lccfn, SVDfn \
= processData(fiber_fn, roi_xml_fn, roi_raw_fn,graphs,\
request.session['graphInvariants'],\
request.session['graphsize'],True)
elif (re.match(re.compile('(s|small)', re.IGNORECASE), graphsize)):
request.session['graphsize'] = 'small'
request.session['smGrfn'], request.session['bgGrfn'], lccfn, SVDfn \
= processData(fiber_fn, roi_xml_fn, roi_raw_fn,graphs, request.session['graphInvariants'], request.session['graphsize'],True)
else:
return django.http.HttpResponseBadRequest(
"Missing graph size. Specify big or small")
# Run invariants
if len(request.session['invariants']) > 0:
print "Computing invariants"
if (request.session['graphsize'] == 'big'):
graph_fn = request.session['bgGrfn']
lcc_fn = request.session['lccfn']
elif (request.session['graphsize'] == 'small'):
graph_fn = request.session['smGrfn']
lcc_fn = None
invariant_fns = runInvariants(request.session['invariants'],\
graph_fn, request.session['graphInvariants'],\
lcc_fn, request.session['graphsize'])
#ret = rzfile.printdir()
#ret = rzfile.testzip()
#ret = rzfile.namelist()
# request.session.clear()
dwnldLoc = "http://mrbrain.cs.jhu.edu" + userDefProjectDir.replace(
' ', '%20')
return HttpResponse(
"Files available for download at " +
dwnldLoc) # change to render of a page with a link to data result
elif (not webargs):
# request.session.clear()
return django.http.HttpResponseBadRequest(
"Expected web arguments to direct project correctly")
else:
# request.session.clear()
return django.http.HttpResponseBadRequest(
"Expected POST data, but none given")
def upload(request, webargs=None):
"""
Programmatic interface for uploading data
@param request: the request object
@param webargs: POST data with userDefProjectName, site, subject, session, scanId, graphsize, [list of invariants to compute] info
"""
# request.session.clear()
if (webargs and request.method == 'POST'):
# Check for malformatted input
webargs = webargs[1:] if webargs.startswith('/') else webargs
webargs = webargs[:-1] if webargs.endswith('/') else webargs
if len(webargs.split('/')) == 7:
[userDefProjectName, site, subject, session, scanId, graphsize, request.session['invariants'] ] = webargs.split('/')
request.session['invariants'] = request.session['invariants'].split(',')
elif len(webargs.split('/')) == 6:
[userDefProjectName, site, subject, session, scanId, graphsize] = webargs.split('/')
userDefProjectDir = adaptProjNameIfReq(os.path.join(settings.MEDIA_ROOT, 'public', userDefProjectName, site, subject, session, scanId))
''' Define data directory paths '''
derivatives, rawdata, graphs, request.session['graphInvariants'], images = defDataDirs(userDefProjectDir)
''' Make appropriate dirs if they dont already exist '''
createDirStruct.createDirStruct([derivatives, rawdata, graphs, request.session['graphInvariants'], images])
print 'Directory structure created...'
uploadFiles = writeBodyToDisk(request.body, derivatives)
# Check which file is which
roi_xml_fn, fiber_fn, roi_raw_fn = filesorter.checkFileExtGengraph(uploadFiles) # Check & sort files
''' Data Processing '''
if (re.match(re.compile('(b|big)', re.IGNORECASE), graphsize)):
request.session['graphsize'] = 'big'
request.session['smGrfn'], request.session['bgGrfn'], lccfn, SVDfn \
= processData(fiber_fn, roi_xml_fn, roi_raw_fn,graphs,\
request.session['graphInvariants'],\
request.session['graphsize'],True)
elif(re.match(re.compile('(s|small)', re.IGNORECASE), graphsize)):
request.session['graphsize'] = 'small'
request.session['smGrfn'], request.session['bgGrfn'], lccfn, SVDfn \
= processData(fiber_fn, roi_xml_fn, roi_raw_fn,graphs, request.session['graphInvariants'], request.session['graphsize'],True)
else:
return django.http.HttpResponseBadRequest ("Missing graph size. Specify big or small")
# Run invariants
if len(request.session['invariants']) > 0:
print "Computing invariants"
if (request.session['graphsize'] == 'big'):
graph_fn = request.session['bgGrfn']
lcc_fn = request.session['lccfn']
elif (request.session['graphsize'] == 'small'):
graph_fn = request.session['smGrfn']
lcc_fn = None
invariant_fns = runInvariants(request.session['invariants'],\
graph_fn, request.session['graphInvariants'],\
lcc_fn, request.session['graphsize'])
#ret = rzfile.printdir()
#ret = rzfile.testzip()
#ret = rzfile.namelist()
# request.session.clear()
dwnldLoc = "http://mrbrain.cs.jhu.edu" + userDefProjectDir.replace(' ','%20')
return HttpResponse ( "Files available for download at " + dwnldLoc) # change to render of a page with a link to data result
elif(not webargs):
# request.session.clear()
return django.http.HttpResponseBadRequest ("Expected web arguments to direct project correctly")
else:
# request.session.clear()
return django.http.HttpResponseBadRequest ("Expected POST data, but none given")