def prepareFiles(request, context):
jobinfo = {}
specimens = []
for lineno, afile in enumerate(request.FILES.getlist('importfile')):
# print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno + 1, 'name',
afile.name, 'size', afile.size)
handle_uploaded_file(afile)
except:
sys.stderr.write("error! file=%s %s" %
(afile.name, traceback.format_exc()))
specimens.append({
'name':
afile.name,
'size':
afile.size,
'error':
'problem uploading file or extracting image metadata, not processed'
})
return jobinfo, specimens
def prepareFiles(request, validateonly):
tricoder_fileinfo = {}
tricoder_files = []
numProblems = 0
for lineno, afile in enumerate(request.FILES.getlist('tricoderfiles')):
# print afile
# we gotta do this for now!
if 'barcode.' not in afile.name: afile.name = 'barcode.' + afile.name
fileinfo = {'id': lineno, 'name': afile.name, 'status': '', 'date': time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())}
# always use the current date as the date for the filename checking
today = time.strftime("%Y-%m-%d", time.localtime())
filenamepattern = r'^barcode.TRIDATA_' + re.escape(today) + r'_[\w_\.]+\.DAT$'
if not re.match(filenamepattern, afile.name):
fileinfo['status'] = 'filename is not valid'
numProblems += 1
else:
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno, 'name', afile.name, 'size', afile.size)
if not validateonly:
handle_uploaded_file(afile)
fileinfo['status'] = 'OK'
except:
if validateonly:
fileinfo['status'] = 'validation failed'
else:
fileinfo['status'] = 'file handling problem, not uploaded'
numProblems += 1
tricoder_files.append(fileinfo)
if numProblems > 0:
errormsg = 'Errors found, abandoning upload. Please fix and try again.'
else:
tricoder_filenumber = time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
tricoder_fileinfo['tricoder_filenumber'] = tricoder_filenumber
tricoder_fileinfo['estimatedtime'] = '%8.1f' % (len(tricoder_files) * 10 / 60.0)
if 'createtricoder' in request.POST:
tricoder_fileinfo['status'] = 'createtricoder'
if not validateonly:
loginfo('start', get_tricoder_file('input',tricoder_filenumber), request)
try:
retcode = subprocess.call(
[POSTBLOBPATH, get_tricoder_file('input',tricoder_filenumber)])
if retcode < 0:
loginfo('process', tricoder_filenumber + " Child was terminated by signal %s" % -retcode,
request)
else:
loginfo('process', tricoder_filenumber + ": Child returned %s" % retcode, request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', get_tricoder_file('input',tricoder_filenumber), request)
elif 'uploadtricoder' in request.POST:
tricoder_fileinfo['status'] = 'uploadtricoder'
else:
tricoder_fileinfo['status'] = 'No status possible'
return tricoder_fileinfo, tricoder_files, numProblems
def import_shapefile_to_simple_locations(request, level=2):
if request.method == 'POST':
form = UploadFileForm(request.POST, request.FILES)
if form.is_valid():
handle_uploaded_file(request.FILES['file'], level)
return HttpResponse("OK")
else:
return HttpResponse("NOTOK")
else:
form = UploadFileForm()
return render_to_response('maintenance/upload.html', {'form': form},
context_instance = RequestContext(request),)
def prepareFiles(request, validateonly):
tricoder_fileinfo = {}
tricoder_files = []
for lineno, afile in enumerate(request.FILES.getlist("tricoderfiles")):
# print afile
try:
print "%s %s: %s %s (%s %s)" % ("id", lineno, "name", afile.name, "size", afile.size)
fileinfo = {"id": lineno, "name": afile.name, "size": afile.size, "date": ""}
if not validateonly:
handle_uploaded_file(afile)
tricoder_files.append(fileinfo)
except:
if not validateonly:
# we still upload the file, anyway...
handle_uploaded_file(afile)
tricoder_files.append(
{"name": afile.name, "size": afile.size, "error": "problem extracting image metadata, not processed"}
)
if len(tricoder_files) > 0:
tricoder_filenumber = time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
tricoder_fileinfo["tricoder_filenumber"] = tricoder_filenumber
tricoder_fileinfo["estimatedtime"] = "%8.1f" % (len(tricoder_files) * 10 / 60.0)
if "createtricoder" in request.POST:
tricoder_fileinfo["status"] = "createtricoder"
if not validateonly:
loginfo("start", get_tricoder_file(tricoder_filenumber), request)
try:
retcode = subprocess.call([POSTBLOBPATH, get_tricoder_file(tricoder_filenumber)])
if retcode < 0:
loginfo(
"process", tricoder_filenumber + " Child was terminated by signal %s" % -retcode, request
)
else:
loginfo("process", tricoder_filenumber + ": Child returned %s" % retcode, request)
except OSError as e:
loginfo("error", "Execution failed: %s" % e, request)
loginfo("finish", get_tricoder_file(tricoder_filenumber), request)
elif "uploadtricoder" in request.POST:
tricoder_fileinfo["status"] = "uploadtricoder"
else:
tricoder_fileinfo["status"] = "No status possible"
return tricoder_fileinfo, tricoder_files
def import_shapefile_to_simple_locations(request, level=2):
if request.method == 'POST':
form = UploadFileForm(request.POST, request.FILES)
if form.is_valid():
handle_uploaded_file(request.FILES['file'], level)
return HttpResponse("OK")
else:
return HttpResponse("NOTOK")
else:
form = UploadFileForm()
return render_to_response(
'maintenance/upload.html',
{'form': form},
context_instance=RequestContext(request),
)
def prepareFiles(request, validateonly):
tricoder_fileinfo = {}
tricoder_files = []
for lineno, afile in enumerate(request.FILES.getlist('tricoderfiles')):
# print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno, 'name', afile.name, 'size', afile.size)
fileinfo = {'id': lineno, 'name': afile.name, 'size': afile.size, 'date': ''}
if not validateonly:
handle_uploaded_file(afile)
tricoder_files.append(fileinfo)
except:
if not validateonly:
# we still upload the file, anyway...
handle_uploaded_file(afile)
tricoder_files.append({'name': afile.name, 'size': afile.size,
'error': 'problem extracting image metadata, not processed'})
if len(tricoder_files) > 0:
tricoder_filenumber = time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
tricoder_fileinfo['tricoder_filenumber'] = tricoder_filenumber
tricoder_fileinfo['estimatedtime'] = '%8.1f' % (len(tricoder_files) * 10 / 60.0)
if 'createtricoder' in request.POST:
tricoder_fileinfo['status'] = 'createtricoder'
if not validateonly:
loginfo('start', get_tricoder_file(tricoder_filenumber), request)
try:
retcode = subprocess.call(
[POSTBLOBPATH, get_tricoder_file(tricoder_filenumber)])
if retcode < 0:
loginfo('process', tricoder_filenumber + " Child was terminated by signal %s" % -retcode, request)
else:
loginfo('process', tricoder_filenumber + ": Child returned %s" % retcode, request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', get_tricoder_file(tricoder_filenumber), request)
elif 'uploadtricoder' in request.POST:
tricoder_fileinfo['status'] = 'uploadtricoder'
else:
tricoder_fileinfo['status'] = 'No status possible'
return tricoder_fileinfo, tricoder_files
def upload(request):
# Handle file upload
if request.method == 'POST':
form = DocumentForm(request.POST, request.FILES)
if form.is_valid():
handle_uploaded_file(request)
# Redirect to the document list after POST
return HttpResponseRedirect(reverse('upload'))
else:
form = DocumentForm() # A empty, unbound form
# Load documents for the summary page sorted by created time
documents = Document.objects.all().order_by('-created_time')
# Render list page with the documents and the form
return render(request, 'upload.html', {
'documents': documents,
'form': form
})
def user_image_upload(request):
# Check authentication
if "username" not in request.session:
return redirect("/login/")
if request.method == 'GET':
form = UploadForm()
return render(request, 'upload.html', { 'title': 'Upload', 'form': form })
elif request.method == 'POST':
form = UploadForm(request.POST, request.FILES)
if not form.is_valid():
return render(request, 'upload.html', { 'title': 'Upload', 'form': form, 'response_message': 'fail' })
# Handle file
fpath = handle_uploaded_file(request.FILES['file_image'])
fname = get_filename(request.FILES['file_image'].name)
# Send file to API
params = {
"id": fname,
"name": form.cleaned_data['appname'],
"status": form.cleaned_data['status'],
"manifest_id": form.cleaned_data['manifest_id'],
"storage_id": form.cleaned_data['storage_id'],
"plugin_id": form.cleaned_data['plugin_id'],
"disk_format": form.cleaned_data['disk_format'],
"container_format": form.cleaned_data['container_format'],
}
files = {"image": open(fpath, 'rb')}
try:
putNewAppToAPI(fname, files, params)
request.session['upload_status'] = 'success'
except requests.exceptions.HTTPError:
return render(request, 'upload.html', { 'title': 'Upload', 'form': form, 'response_message': 'fail' })
# Delete file
os.remove(fpath)
return redirect('/store/')
def add_pic_to_person(request):
# validate if this user owns this profile, then only she can add picture to this profile.
if 'person_id' not in request.GET:
raise Http404
objs = MissingPerson.objects.filter(reporting_user_id=request.user.id, id=request.GET['person_id'])
if objs is None:
raise Http404
'''
Steps:
1. Detect Face in picture.
2. Save the picture locally
3. Add the picture in FaceMatcher module to person.
'''
try:
matcher = utils.handle_uploaded_file(request)
utils.add_source_picture(request.GET['person_id'],matcher)
except Exception as e:
raise Http404(e)
return HttpResponse("done")
def upload(request):
if request.method == 'POST' and 'Upload' in request.POST:
form1 = UploadForm1(request.POST, request.FILES)
form2 = UploadForm2(request.POST, request.FILES)
form3 = UploadForm3(request.POST, request.FILES)
form4 = UploadForm4(request.POST, request.FILES)
form5 = UploadForm5(request.POST, request.FILES)
p_uuid = uuid4().hex
date = datetime.date.today().isoformat()
dest = "/".join(["uploads", str(p_uuid)])
if form1.is_valid():
if form2.is_valid():
project = ".".join(["project", "csv"])
file1 = request.FILES['docfile1']
handle_uploaded_file(file1, dest, project)
parse_project(dest, date, file1, p_uuid)
print("Parsed project!")
sample = ".".join(["sample", "csv"])
file2 = request.FILES['docfile2']
handle_uploaded_file(file2, dest, sample)
parse_sample(file2, p_uuid)
print("Parsed sample!")
taxonomy = ".".join(["mothur", "taxonomy"])
file3 = request.FILES['docfile3']
handle_uploaded_file(file3, dest, taxonomy)
parse_taxonomy(file3)
print("Parsed taxonomy!")
shared = ".".join(["mothur", "shared"])
file4 = request.FILES['docfile4']
handle_uploaded_file(file4, dest, shared)
parse_profile(dest, p_uuid)
print("Parsed profile!")
#taxaprofile(p_uuid)
#print("Taxa profiles created")
elif form3.is_valid():
name = ".".join(["project", "csv"])
file = request.FILES['docfile1']
handle_uploaded_file(file, dest, name)
name = ".".join(["sample", "csv"])
file = request.FILES['docfile2']
handle_uploaded_file(file, dest, name)
name = ".".join(["biom_1.5", "txt"])
file = request.FILES['docfile5']
handle_uploaded_file(file, dest, name)
elif form4.is_valid():
name = ".".join(["project", "csv"])
file = request.FILES['docfile1']
handle_uploaded_file(file, dest, name)
name = ".".join(["sample", "csv"])
file = request.FILES['docfile2']
handle_uploaded_file(file, dest, name)
name = ".".join(["biom_1.4", "txt"])
file = request.FILES['docfile6']
handle_uploaded_file(file, dest, name)
elif form5.is_valid():
name = ".".join(["project", "csv"])
file = request.FILES['docfile1']
handle_uploaded_file(file, dest, name)
name = ".".join(["sample", "csv"])
file = request.FILES['docfile2']
handle_uploaded_file(file, dest, name)
name = ".".join(["biom_1.4", "txt"])
file = request.FILES['docfile7']
handle_uploaded_file(file, dest, name)
else:
print("Please upload taxonomic profile data")
else:
print("Please upload meta files")
elif request.method == 'POST' and 'clickMe' in request.POST:
remove_list(request)
projects = Project.objects.all().order_by('project_name')
return render_to_response('upload.html', {
'projects': projects,
'form1': UploadForm1,
'form2': UploadForm2,
'form3': UploadForm3,
'form4': UploadForm4,
'form5': UploadForm5
},
context_instance=RequestContext(request))
def save(self):
self.folder, root_path = get_root_path(self.folder_name)
name = self.cleaned_data["file"].name
self.filename, self.path = get_file_path(name, root_path)
handle_uploaded_file(self.cleaned_data["file"], self.path)
def uploadfiles(request):
jobinfo = {}
constants = {}
images = []
dropdowns = getDropdowns()
elapsedtime = time.time()
form = forms.Form(request)
if request.POST:
contributor = request.POST['contributor']
overrideContributor = request.POST['overridecreator']
creatorDisplayname = request.POST['creator']
overrideCreator = request.POST['overridecreator']
rightsholderDisplayname = request.POST['rightsholder']
overrideRightsholder = request.POST['overriderightsholder']
constants = {'creator': creatorDisplayname, 'contributor': contributor, 'rightsholder': rightsholderDisplayname}
for lineno,afile in enumerate(request.FILES.getlist('imagefiles')):
#print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno, 'name', afile.name, 'size', afile.size)
im = get_exif(afile)
objectnumber = getNumber(afile.name)
#objectCSID = getCSID(objectnumber)
creator, creatorRefname = assignValue(creatorDisplayname,overrideCreator,im,'Artist',dropdowns['creators'])
contributor, dummy = assignValue(contributor,overrideContributor,im,'ImageDescription',{})
rightsholder, rightsholderRefname = assignValue(rightsholderDisplayname,overrideRightsholder,im,'RightsHolder',dropdowns['rightsholders'])
datetimedigitized, dummy = assignValue('','ifblank',im,'DateTimeDigitized',{})
imageinfo = {'id': lineno, 'name': afile.name, 'size': afile.size,
'objectnumber': objectnumber,
#'objectCSID': objectCSID,
'date': datetimedigitized,
'creator': creatorRefname,
'contributor': contributor,
'rightsholder': rightsholderRefname,
'creatorDisplayname': creator,
'rightsholderDisplayname': rightsholder,
'contributorDisplayname': contributor
}
handle_uploaded_file(afile, imageinfo)
images.append(imageinfo)
except:
#raise
images.append({'name': afile.name, 'size': afile.size, 'error': 'problem extracting image metadata, not processed'})
if len(images) > 0:
jobnumber = time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
jobinfo['jobnumber'] = jobnumber
writeCsv(getJobfile(jobnumber)+'.step1.csv', images,
['name', 'size', 'objectnumber', 'date', 'creator', 'contributor', 'rightsholder'])
jobinfo['estimatedtime'] = '%8.1f' % (len(images) * 10 / 60.0)
if 'createmedia' in request.POST:
jobinfo['status'] = 'createmedia'
loginfo('start', getJobfile(jobnumber), request)
try:
retcode = subprocess.call(["/usr/local/share/django/pahma_project/uploadmedia/postblob.sh", getJobfile(jobnumber)])
if retcode < 0:
loginfo('process', jobnumber+" Child was terminated by signal %s" % -retcode, request)
else:
loginfo('process', jobnumber+": Child returned %s" % retcode, request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', getJobfile(jobnumber), request)
elif 'uploadmedia' in request.POST:
jobinfo['status'] = 'uploadmedia'
else:
jobinfo['status'] = 'No status possible'
status = 'up'
timestamp = time.strftime("%b %d %Y %H:%M:%S", time.localtime())
elapsedtime = time.time() - elapsedtime
return render(request, 'uploadmedia.html',
{'title': TITLE, 'images': images, 'count': len(images), 'constants': constants, 'jobinfo': jobinfo,
'dropdowns': dropdowns, 'overrides': overrides, 'status': status, 'timestamp': timestamp, 'elapsedtime': '%8.2f' % elapsedtime})
def prepareFiles(request, validateonly):
tricoder_fileinfo = {}
tricoder_files = []
numProblems = 0
for lineno, afile in enumerate(request.FILES.getlist('tricoderfiles')):
# print afile
# we gotta do this for now!
if 'barcode.' not in afile.name: afile.name = 'barcode.' + afile.name
fileinfo = {
'id': lineno,
'name': afile.name,
'status': '',
'date': time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
}
# always use the current date as the date for the filename checking
today = time.strftime("%Y-%m-%d", time.localtime())
filenamepattern = r'^barcode.TRIDATA_' + re.escape(
today) + r'_[\w_\.]+\.DAT$'
if not re.match(filenamepattern, afile.name):
fileinfo['status'] = 'filename is not valid'
numProblems += 1
else:
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno, 'name',
afile.name, 'size', afile.size)
if not validateonly:
handle_uploaded_file(afile)
fileinfo['status'] = 'OK'
except:
if validateonly:
fileinfo['status'] = 'validation failed'
else:
fileinfo['status'] = "error! %s" % traceback.format_exc()
sys.stderr.write("error! %s" % traceback.format_exc())
numProblems += 1
tricoder_files.append(fileinfo)
if numProblems > 0:
errormsg = 'Errors found, abandoning upload. Please fix and try again.'
else:
tricoder_filenumber = time.strftime("%Y-%m-%d-%H-%M-%S",
time.localtime())
tricoder_fileinfo['tricoder_filenumber'] = tricoder_filenumber
tricoder_fileinfo['estimatedtime'] = '%8.1f' % (len(tricoder_files) *
10 / 60.0)
if 'createtricoder' in request.POST:
tricoder_fileinfo['status'] = 'createtricoder'
if not validateonly:
loginfo('start', get_tricoder_file('input',
tricoder_filenumber),
request)
try:
retcode = subprocess.call([
POSTBLOBPATH,
get_tricoder_file('input', tricoder_filenumber)
])
if retcode < 0:
loginfo(
'process', tricoder_filenumber +
" Child was terminated by signal %s" % -retcode,
request)
else:
loginfo(
'process', tricoder_filenumber +
": Child returned %s" % retcode, request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish',
get_tricoder_file('input', tricoder_filenumber),
request)
elif 'uploadtricoder' in request.POST:
tricoder_fileinfo['status'] = 'uploadtricoder'
else:
tricoder_fileinfo['status'] = 'No status possible'
return tricoder_fileinfo, tricoder_files, numProblems
def prepareFiles(request, validateonly, BMUoptions, constants):
jobnumber = constants['jobnumber']
jobinfo = {}
images = []
for lineno, afile in enumerate(request.FILES.getlist('imagefiles')):
# print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno + 1, 'name', afile.name, 'size', afile.size)
image = get_exif(afile)
filename, objectnumber, imagenumber = getNumber(afile.name, INSTITUTION)
datetimedigitized, dummy = assignValue('', 'ifblank', image, 'DateTimeDigitized', {})
imageinfo = {'id': lineno, 'name': afile.name, 'size': afile.size,
'objectnumber': objectnumber,
'imagenumber': imagenumber,
# 'objectCSID': objectCSID,
'date': datetimedigitized}
for override in BMUoptions['overrides']:
dname,refname = assignValue(constants[override[2]][0], constants[override[2]][1], image, override[3], override[4])
imageinfo[override[2]] = refname
# add the Displayname just in case...
imageinfo['%sDisplayname' % override[2]] = dname
if not validateonly:
handle_uploaded_file(afile)
for option in ['handling', 'approvedforweb']:
if option in request.POST:
imageinfo[option] = request.POST[option]
else:
imageinfo[option] = ''
if 'handling' in request.POST:
handling = request.POST['handling']
for parms in BMUoptions['bmuconstants'][handling]:
imageinfo[parms] = BMUoptions['bmuconstants'][handling][parms]
# special case:
# borndigital media have their mh id numbers unconditionally replaced with a sequence number
if imageinfo['handling'] == 'borndigital':
# for these, we create a media handling number...
# options considered were:
# DP-2015-10-08-12-16-43-0001 length: 27
# DP-201510081216430001 length: 21
# DP-2CBE859E990BFB1 length: 18
# DP-2015-10-08-12-16-43-0001 length: 27 the winner! (most legible)
mhnumber = jobnumber + ("-%0.4d" % (lineno + 1))
#mhnumber = hex(int(mhnumber.replace('-','')))[2:]
imageinfo['objectnumber'] = 'DP-' + mhnumber
images.append(imageinfo)
except:
# raise
if not validateonly:
# we still upload the file, anyway...
handle_uploaded_file(afile)
images.append({'name': afile.name, 'size': afile.size,
'error': 'problem extracting image metadata, not processed'})
if len(images) > 0:
jobinfo['jobnumber'] = jobnumber
if not validateonly:
writeCsv(getJobfile(jobnumber) + '.step1.csv', images, FIELDS2WRITE)
jobinfo['estimatedtime'] = '%8.1f' % (len(images) * 10 / 60.0)
if 'createmedia' in request.POST:
jobinfo['status'] = 'createmedia'
if not validateonly:
loginfo('start', getJobfile(jobnumber), request)
try:
retcode = subprocess.call([path.join(POSTBLOBPATH, 'postblob.sh'), INSTITUTION, getJobfile(jobnumber), BATCHPARAMETERS])
if retcode < 0:
loginfo('process', jobnumber + " Child was terminated by signal %s" % -retcode, request)
else:
loginfo('process', jobnumber + ": Child returned %s" % retcode, request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', getJobfile(jobnumber), request)
elif 'uploadmedia' in request.POST:
jobinfo['status'] = 'uploadmedia'
else:
jobinfo['status'] = 'No status possible'
return jobinfo, images
def prepareFiles(request, validateonly, BMUoptions, constants):
jobnumber = constants['jobnumber']
jobinfo = {}
images = []
for lineno, afile in enumerate(request.FILES.getlist('imagefiles')):
# print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno + 1, 'name', afile.name, 'size', afile.size)
image = get_exif(afile)
filename, objectnumber, imagenumber = getNumber(afile.name, INSTITUTION)
datetimedigitized, dummy = assignValue('', 'ifblank', image, 'DateTimeDigitized', {})
imageinfo = {'id': lineno, 'name': afile.name, 'size': afile.size,
'objectnumber': objectnumber,
'imagenumber': imagenumber,
# 'objectCSID': objectCSID,
'date': datetimedigitized}
for override in BMUoptions['overrides']:
dname,refname = assignValue(constants[override[2]][0], constants[override[2]][1], image, override[3], override[4])
imageinfo[override[2]] = refname
# add the Displayname just in case...
imageinfo['%sDisplayname' % override[2]] = dname
if not validateonly:
handle_uploaded_file(afile)
for option in ['handling', 'approvedforweb']:
if option in request.POST:
imageinfo[option] = request.POST[option]
else:
imageinfo[option] = ''
if 'handling' in request.POST:
handling = request.POST['handling']
for parms in BMUoptions['bmuconstants'][handling]:
imageinfo[parms] = BMUoptions['bmuconstants'][handling][parms]
# special case:
# borndigital media have their mh id numbers unconditionally replaced with a sequence number
if imageinfo['handling'] == 'borndigital':
# for these, we create a media handling number...
# options considered were:
# DP-2015-10-08-12-16-43-0001 length: 27
# DP-201510081216430001 length: 21
# DP-2CBE859E990BFB1 length: 18
# DP-2cbe859e990bfb1 length: 18 the winner!
mhnumber = jobnumber + ("-%0.4d" % (lineno + 1))
#mhnumber = hex(int(mhnumber.replace('-','')))[2:]
imageinfo['objectnumber'] = 'DP-' + mhnumber
images.append(imageinfo)
except:
# raise
if not validateonly:
# we still upload the file, anyway...
handle_uploaded_file(afile)
images.append({'name': afile.name, 'size': afile.size,
'error': 'problem extracting image metadata, not processed'})
if len(images) > 0:
jobinfo['jobnumber'] = jobnumber
if not validateonly:
writeCsv(getJobfile(jobnumber) + '.step1.csv', images, FIELDS2WRITE)
jobinfo['estimatedtime'] = '%8.1f' % (len(images) * 10 / 60.0)
if 'createmedia' in request.POST:
jobinfo['status'] = 'createmedia'
if not validateonly:
loginfo('start', getJobfile(jobnumber), request)
try:
retcode = subprocess.call([path.join(POSTBLOBPATH, 'postblob.sh'), INSTITUTION, getJobfile(jobnumber), BATCHPARAMETERS])
if retcode < 0:
loginfo('process', jobnumber + " Child was terminated by signal %s" % -retcode, request)
else:
loginfo('process', jobnumber + ": Child returned %s" % retcode, request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', getJobfile(jobnumber), request)
elif 'uploadmedia' in request.POST:
jobinfo['status'] = 'uploadmedia'
else:
jobinfo['status'] = 'No status possible'
return jobinfo, images
def upload(request):
if request.method == "POST" and "Upload" in request.POST:
form1 = UploadForm1(request.POST, request.FILES)
form2 = UploadForm2(request.POST, request.FILES)
form3 = UploadForm3(request.POST, request.FILES)
form4 = UploadForm4(request.POST, request.FILES)
form5 = UploadForm5(request.POST, request.FILES)
p_uuid = uuid4().hex
date = datetime.date.today().isoformat()
dest = "/".join(["uploads", str(p_uuid)])
if form1.is_valid():
if form2.is_valid():
project = ".".join(["project", "csv"])
file1 = request.FILES["docfile1"]
handle_uploaded_file(file1, dest, project)
parse_project(dest, date, file1, p_uuid)
print("Parsed project!")
sample = ".".join(["sample", "csv"])
file2 = request.FILES["docfile2"]
handle_uploaded_file(file2, dest, sample)
parse_sample(file2, p_uuid)
print("Parsed sample!")
taxonomy = ".".join(["mothur", "taxonomy"])
file3 = request.FILES["docfile3"]
handle_uploaded_file(file3, dest, taxonomy)
parse_taxonomy(file3)
print("Parsed taxonomy!")
shared = ".".join(["mothur", "shared"])
file4 = request.FILES["docfile4"]
handle_uploaded_file(file4, dest, shared)
parse_profile(dest, p_uuid)
print("Parsed profile!")
# taxaprofile(p_uuid)
# print("Taxa profiles created")
elif form3.is_valid():
name = ".".join(["project", "csv"])
file = request.FILES["docfile1"]
handle_uploaded_file(file, dest, name)
name = ".".join(["sample", "csv"])
file = request.FILES["docfile2"]
handle_uploaded_file(file, dest, name)
name = ".".join(["biom_1.5", "txt"])
file = request.FILES["docfile5"]
handle_uploaded_file(file, dest, name)
elif form4.is_valid():
name = ".".join(["project", "csv"])
file = request.FILES["docfile1"]
handle_uploaded_file(file, dest, name)
name = ".".join(["sample", "csv"])
file = request.FILES["docfile2"]
handle_uploaded_file(file, dest, name)
name = ".".join(["biom_1.4", "txt"])
file = request.FILES["docfile6"]
handle_uploaded_file(file, dest, name)
elif form5.is_valid():
name = ".".join(["project", "csv"])
file = request.FILES["docfile1"]
handle_uploaded_file(file, dest, name)
name = ".".join(["sample", "csv"])
file = request.FILES["docfile2"]
handle_uploaded_file(file, dest, name)
name = ".".join(["biom_1.4", "txt"])
file = request.FILES["docfile7"]
handle_uploaded_file(file, dest, name)
else:
print("Please upload taxonomic profile data")
else:
print("Please upload meta files")
elif request.method == "POST" and "clickMe" in request.POST:
remove_list(request)
projects = Project.objects.all().order_by("project_name")
return render_to_response(
"upload.html",
{
"projects": projects,
"form1": UploadForm1,
"form2": UploadForm2,
"form3": UploadForm3,
"form4": UploadForm4,
"form5": UploadForm5,
},
context_instance=RequestContext(request),
)
def uploadfiles(request):
jobinfo = {}
constants = {}
images = []
dropdowns = getDropdowns()
elapsedtime = time.time()
form = forms.Form(request)
if request.POST:
contributor = request.POST['contributor']
overrideContributor = request.POST['overridecreator']
creatorDisplayname = request.POST['creator']
overrideCreator = request.POST['overridecreator']
rightsholderDisplayname = request.POST['rightsholder']
overrideRightsholder = request.POST['overriderightsholder']
constants = {
'creator': creatorDisplayname,
'contributor': contributor,
'rightsholder': rightsholderDisplayname
}
for lineno, afile in enumerate(request.FILES.getlist('imagefiles')):
#print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno, 'name',
afile.name, 'size', afile.size)
im = get_exif(afile)
objectnumber = getNumber(afile.name)
#objectCSID = getCSID(objectnumber)
creator, creatorRefname = assignValue(creatorDisplayname,
overrideCreator, im,
'Artist',
dropdowns['creators'])
contributor, dummy = assignValue(contributor,
overrideContributor, im,
'ImageDescription', {})
rightsholder, rightsholderRefname = assignValue(
rightsholderDisplayname, overrideRightsholder, im,
'RightsHolder', dropdowns['rightsholders'])
datetimedigitized, dummy = assignValue('', 'ifblank', im,
'DateTimeDigitized', {})
imageinfo = {
'id': lineno,
'name': afile.name,
'size': afile.size,
'objectnumber': objectnumber,
#'objectCSID': objectCSID,
'date': datetimedigitized,
'creator': creatorRefname,
'contributor': contributor,
'rightsholder': rightsholderRefname,
'creatorDisplayname': creator,
'rightsholderDisplayname': rightsholder,
'contributorDisplayname': contributor
}
handle_uploaded_file(afile, imageinfo)
images.append(imageinfo)
except:
#raise
images.append({
'name':
afile.name,
'size':
afile.size,
'error':
'problem extracting image metadata, not processed'
})
if len(images) > 0:
jobnumber = time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
jobinfo['jobnumber'] = jobnumber
writeCsv(
getJobfile(jobnumber) + '.step1.csv', images, [
'name', 'size', 'objectnumber', 'date', 'creator',
'contributor', 'rightsholder'
])
jobinfo['estimatedtime'] = '%8.1f' % (len(images) * 10 / 60.0)
if 'createmedia' in request.POST:
jobinfo['status'] = 'createmedia'
loginfo('start', getJobfile(jobnumber), request)
try:
retcode = subprocess.call([
"/usr/local/share/django/pahma_project/uploadmedia/postblob.sh",
getJobfile(jobnumber)
])
if retcode < 0:
loginfo(
'process', jobnumber +
" Child was terminated by signal %s" % -retcode,
request)
else:
loginfo('process',
jobnumber + ": Child returned %s" % retcode,
request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', getJobfile(jobnumber), request)
elif 'uploadmedia' in request.POST:
jobinfo['status'] = 'uploadmedia'
else:
jobinfo['status'] = 'No status possible'
status = 'up'
timestamp = time.strftime("%b %d %Y %H:%M:%S", time.localtime())
elapsedtime = time.time() - elapsedtime
return render(
request, 'uploadmedia.html', {
'title': TITLE,
'images': images,
'count': len(images),
'constants': constants,
'jobinfo': jobinfo,
'dropdowns': dropdowns,
'overrides': overrides,
'status': status,
'timestamp': timestamp,
'elapsedtime': '%8.2f' % elapsedtime
})
def prepareFiles(request, validateonly, dropdowns):
jobinfo = {}
images = []
for lineno, afile in enumerate(request.FILES.getlist('imagefiles')):
# print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno, 'name', afile.name,
'size', afile.size)
image = get_exif(afile)
filename, objectnumber, imagenumber = getNumber(afile.name)
# objectCSID = getCSID(objectnumber)
im.creator, im.creatorRefname = assignValue(
im.creatorDisplayname, im.overrideCreator, image, 'Artist',
dropdowns['creators'])
im.contributor, dummy = assignValue(im.contributor,
im.overrideContributor, image,
'ImageDescription', {})
im.rightsholder, im.rightsholderRefname = assignValue(
im.rightsholderDisplayname, im.overrideRightsholder, image,
'RightsHolder', dropdowns['rightsholders'])
datetimedigitized, dummy = assignValue('', 'ifblank', image,
'DateTimeDigitized', {})
imageinfo = {
'id': lineno,
'name': afile.name,
'size': afile.size,
'objectnumber': objectnumber,
'imagenumber': imagenumber,
# 'objectCSID': objectCSID,
'date': datetimedigitized,
'creator': im.creatorRefname,
'contributor': im.contributor,
'rightsholder': im.rightsholderRefname,
'creatorDisplayname': im.creator,
'rightsholderDisplayname': im.rightsholder,
'contributorDisplayname': im.contributor
}
if not validateonly:
handle_uploaded_file(afile)
images.append(imageinfo)
except:
if not validateonly:
# we still upload the file, anyway...
handle_uploaded_file(afile)
images.append({
'name':
afile.name,
'size':
afile.size,
'error':
'problem extracting image metadata, not processed'
})
if len(images) > 0:
jobnumber = time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
jobinfo['jobnumber'] = jobnumber
if not validateonly:
writeCsv(
getJobfile(jobnumber) + '.step1.csv', images, [
'name', 'size', 'objectnumber', 'date', 'creator',
'contributor', 'rightsholder', 'imagenumber'
])
jobinfo['estimatedtime'] = '%8.1f' % (len(images) * 10 / 60.0)
if 'createmedia' in request.POST:
jobinfo['status'] = 'createmedia'
if not validateonly:
loginfo('start', getJobfile(jobnumber), request)
try:
retcode = subprocess.call([
path.join(POSTBLOBPATH, 'postblob.sh'),
getJobfile(jobnumber)
])
if retcode < 0:
loginfo(
'process', jobnumber +
" Child was terminated by signal %s" % -retcode,
request)
else:
loginfo('process',
jobnumber + ": Child returned %s" % retcode,
request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', getJobfile(jobnumber), request)
elif 'uploadmedia' in request.POST:
jobinfo['status'] = 'uploadmedia'
else:
jobinfo['status'] = 'No status possible'
return jobinfo, images
def prepareFiles(request, validateonly, dropdowns):
jobinfo = {}
images = []
for lineno, afile in enumerate(request.FILES.getlist('imagefiles')):
# print afile
try:
print "%s %s: %s %s (%s %s)" % ('id', lineno, 'name', afile.name, 'size', afile.size)
image = get_exif(afile)
filename, objectnumber, imagenumber = getNumber(afile.name)
# objectCSID = getCSID(objectnumber)
im.creator, im.creatorRefname = assignValue(im.creatorDisplayname, im.overrideCreator, image, 'Artist',
dropdowns['creators'])
im.contributor, dummy = assignValue(im.contributor, im.overrideContributor, image, 'ImageDescription', {})
im.rightsholder, im.rightsholderRefname = assignValue(im.rightsholderDisplayname, im.overrideRightsholder,
image, 'RightsHolder', dropdowns['rightsholders'])
datetimedigitized, dummy = assignValue('', 'ifblank', image, 'DateTimeDigitized', {})
imageinfo = {'id': lineno, 'name': afile.name, 'size': afile.size,
'objectnumber': objectnumber,
'imagenumber': imagenumber,
# 'objectCSID': objectCSID,
'date': datetimedigitized,
'creator': im.creatorRefname,
'contributor': im.contributor,
'rightsholder': im.rightsholderRefname,
'creatorDisplayname': im.creator,
'rightsholderDisplayname': im.rightsholder,
'contributorDisplayname': im.contributor
}
if not validateonly:
handle_uploaded_file(afile)
images.append(imageinfo)
except:
if not validateonly:
# we still upload the file, anyway...
handle_uploaded_file(afile)
images.append({'name': afile.name, 'size': afile.size,
'error': 'problem extracting image metadata, not processed'})
if len(images) > 0:
jobnumber = time.strftime("%Y-%m-%d-%H-%M-%S", time.localtime())
jobinfo['jobnumber'] = jobnumber
if not validateonly:
writeCsv(getJobfile(jobnumber) + '.step1.csv', images,
['name', 'size', 'objectnumber', 'date', 'creator', 'contributor', 'rightsholder', 'imagenumber'])
jobinfo['estimatedtime'] = '%8.1f' % (len(images) * 10 / 60.0)
if 'createmedia' in request.POST:
jobinfo['status'] = 'createmedia'
if not validateonly:
loginfo('start', getJobfile(jobnumber), request)
try:
retcode = subprocess.call([path.join(POSTBLOBPATH, 'postblob.sh'), getJobfile(jobnumber)])
if retcode < 0:
loginfo('process', jobnumber + " Child was terminated by signal %s" % -retcode, request)
else:
loginfo('process', jobnumber + ": Child returned %s" % retcode, request)
except OSError as e:
loginfo('error', "Execution failed: %s" % e, request)
loginfo('finish', getJobfile(jobnumber), request)
elif 'uploadmedia' in request.POST:
jobinfo['status'] = 'uploadmedia'
else:
jobinfo['status'] = 'No status possible'
return jobinfo, images
def check_if_missing(request):
matcher = utils.handle_uploaded_file(request)
matcher.match()
pass