def upload(self):
""" VIEW: Upload page """
if session.get('user_name'):
form = FileForm()
if request.method == 'POST':
if form.validate():
try:
file = form.file.data
file_name = secure_filename(file.filename)
if form.path.data:
if os.path.isdir(form.path.data):
file.save(form.path.data, file_name)
else:
os.makedirs(form.path.data)
file.save(form.path.data, file_name)
else:
file.save(
os.path.join(app.config['UPLOAD_FOLDER'],
file_name))
flash('File uploaded successfully.', 'success')
except Exception as exc:
flash('File upload failed: ' + str(exc), 'danger')
else:
flash('Invalid file!', 'warning')
return self.render('admin/upload.html', form=form)
else:
return redirect(url_for('view_index'))
def import_bookmark(request, template_name='bookmark/import_bookmark.html'):
file_form = FileForm(request.POST or None, request.FILES or None)
if request.method == 'POST' and file_form.is_valid():
file = request.FILES['file']
tags_input = file_form.cleaned_data['tags']
public = file_form.cleaned_data['public']
try:
bookmarks = parse_firefox_bookmark(file)
for bk in bookmarks:
try:
bookmark = Bookmark.objects.create(url=bk['url'],
title=bk['title'],
owner=request.user,
public=public)
if tags_input:
tags = tags_input
else:
tags = parse_tags(bk['tags'])
for tag in tags:
bookmark.tags.add(tag)
# Update the screen shot
update_bk_screen_shot_async(bookmark)
except Exception:
pass
return HttpResponseRedirect(reverse("my_bookmark"))
except Exception, e:
file_form._errors[NON_FIELD_ERRORS] = ErrorList([e.message])
def upload(req):
up_files = 'yes'
if req.method == "POST":
ff = FileForm(req.POST, req.FILES)
folder_name = req.session.get('folder_name')
if ff.is_valid():
#获取表单数据
b = ' Byte'
file_name = ff.cleaned_data['file_name']
file_loc = ff.cleaned_data['file_loc']
file_handel = req.FILES['file_loc']
file_size = str(file_handel.size) + b
file_type_split1 = str(file_handel.name)
file_type_split2 = file_type_split1.split('.')
file_type = file_type_split2[1]
#写入数据库
upload_time = timezone.now()
f = Folder.objects.get(folder_name=folder_name)
f.modify_time = upload_time
f.save()
f.file_set.create(file_name=file_name,
file_loc=file_loc,
file_size=file_size,
file_type=file_type,
upload_time=upload_time)
return HttpResponseRedirect('/online/index/')
else:
ff = FileForm()
return render(req, 'create_folder_new.html', {
'ff': ff,
'up_files': up_files
})
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 10*1024*1024:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if(form.is_valid()):
#set up parameters for database insert
fileObj = request.FILES['file']
projID = project_api.get_project(projectID)
fname = fileObj.name
fileUUID = str(uuid.uuid4())
#rename file object to have UUID as name to avoid conflicts when retrieving files
fileObj.name=fileUUID
f = ProjectFile(file=fileObj,
project=projID,
name=fname,
uuid=fileUUID)
f.save()
return redirect(request.POST['referer'])
def upload(req):
up_files = 'yes'
if req.method == "POST":
ff = FileForm(req.POST, req.FILES)
folder_name = req.session.get('folder_name')
if ff.is_valid():
#获取表单数据
b = ' Byte'
file_name = ff.cleaned_data['file_name']
file_loc = ff.cleaned_data['file_loc']
file_handel = req.FILES['file_loc']
file_size = str(file_handel.size) + b
file_type_split1 = str(file_handel.name)
file_type_split2 = file_type_split1.split('.')
file_type = file_type_split2[1]
#写入数据库
upload_time = timezone.now()
f = Folder.objects.get(folder_name=folder_name)
f.modify_time = upload_time
f.save()
f.file_set.create(file_name=file_name, file_loc=file_loc, file_size=file_size, file_type=file_type, upload_time=upload_time)
return HttpResponseRedirect('/online/index/')
else:
ff = FileForm()
return render(req, 'create_folder_new.html', {'ff': ff, 'up_files': up_files})
def edit_photos():
upload = FileForm()
set_loop = Set.query.order_by(Set.id.desc()).all()
if upload.validate_on_submit():
for loop in set_loop:
if request.form["select_set"] == loop.tag:
file = request.files['file']
bucket.put_object(Key='Tractor Show/' + loop.name + '/' +
file.filename,
Body=file)
newFile = Images(name=file.filename, set=loop)
db.session.add(newFile)
db.session.commit()
return redirect('/dashboard/photos#' + loop.tag)
add_set = AddSet()
if add_set.validate_on_submit():
render_tag = tag_generator(request.form["set"])
new_set = Set(name=request.form["set"], tag=render_tag)
db.session.add(new_set)
db.session.commit()
return redirect(url_for('edit_photos'))
return render_template('authentication/edit-photos.html',
upload=upload,
add_set=add_set,
set_loop=set_loop,
s3projects=s3projects)
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 10 * 1024 * 1024:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if (form.is_valid()):
#set up parameters for database insert
fileObj = request.FILES['file']
projID = project_api.get_project(projectID)
fname = fileObj.name
fileUUID = str(uuid.uuid4())
#rename file object to have UUID as name to avoid conflicts when retrieving files
fileObj.name = fileUUID
f = ProjectFile(file=fileObj,
project=projID,
name=fname,
uuid=fileUUID)
f.save()
return redirect(request.POST['referer'])
def investing(request):
# Handle file upload
file_form = FileForm(request.POST)
form = DocumentForm(request.POST, request.FILES)
if request.method == 'POST' and "uploadFile" in request.POST:
# Upload
if form.is_valid():
newdoc = Document(docfile = request.FILES['docfile'])
newdoc.save()
# Redirect to the document list after POST
return HttpResponseRedirect(reverse('dataloader.views.investing'))
elif request.method == 'POST' and "invest" in request.POST:
# Make Investments
if file_form.is_valid():
file_name = file_form.cleaned_data['file_input']
print "### FILE FOR INVESTMENTS: " + file_name
file_path = settings.MEDIA_ROOT + "/" + file_name
print file_path
cr = csv.reader(open(file_path))
# Starting from second row
for row in cr:
if row[0] == 'fund' or row[0] == 'individual':
investment_manager.fund(row)
elif row[0] == 'buy':
investment_manager.buy(row)
elif row[0] == 'sell':
investment_manager.sell(row)
elif row[0] == 'sellbuy':
investment_manager.sellbuy(row)
return HttpResponseRedirect(reverse('dataloader.views.investing'))
elif request.method == 'POST' and "clear" in request.POST:
# Clear Investments
print "### This should clear everything"
Activity.objects.all().delete()
StakeHold.objects.all().delete()
Port_Indi.objects.all().delete()
print "### OK check porfolio page"
else:
form = DocumentForm() # A empty, unbound form
file_form = FileForm()
# Load documents for the list page
documents = Document.objects.all()
return render_to_response(
'nav/investing.html',
{'documents': documents, 'form': form, 'file_form':file_form},
context_instance=RequestContext(request)
)
def hello():
form = FileForm()
if form.validate_on_submit():
f = request.files['file']
f.save(secure_filename('test.pdf'))
Parse()
flash('Parsed successfully', 'success')
return redirect('/')
return render_template('index.html', title='Pdf Parser', form=form)
def update_log(request):
if request.method == "POST":
form = FileForm(request.POST, request.FILES)
if form.is_valid():
cd = form.cleaned_data
handle_uploaded_file(cd)
return HttpResponse("Ok: File %s update success." % cd['name'])
else:
return HttpResponseBadRequest("<h1>Need more arguments</h1>")
else:
return HttpResponseBadRequest("<h1>Wrong request type</h1>")
def index():
form = FileForm()
if form.validate_on_submit():
filename = secure_filename(form.file.data.filename)
print(filename)
if filename.split('.')[1] in ALLOWED_EXT:
form.file.data.save('uploads/' + filename)
else:
flash('Incorrect format selected, please try again!')
return redirect(url_for('index'))
return render_template('index.html', form=form)
def upload_file(request, upload_path=None, upload_link=None):
form = FileForm(request.POST, request.FILES)
if form.is_valid():
uploaded_file = form.cleaned_data['file']
path = os.path.join(upload_path or UPLOAD_PATH, uploaded_file.name)
image_path = default_storage.save(path, uploaded_file)
image_url = default_storage.url(image_path)
if upload_link:
return HttpResponse(image_url)
return HttpResponse(json.dumps({'filelink': image_url, 'filename': uploaded_file.name}))
return HttpResponseForbidden()
def upload_file(request, upload_path=None, upload_link=None):
form = FileForm(request.POST, request.FILES)
if form.is_valid():
uploaded_file = form.cleaned_data['file']
path = os.path.join(upload_path or UPLOAD_PATH, uploaded_file.name)
image_path = default_storage.save(path, uploaded_file)
image_url = default_storage.url(image_path)
if upload_link:
return HttpResponse(image_url)
return HttpResponse(json.dumps({'filelink': image_url, 'filename': uploaded_file.name}))
return HttpResponseForbidden()
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 1100000:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if(form.is_valid()):
file = request.FILES['file']
f = ProjectFile(project = project_api.get_project(projectID), file = file, name = file.name)
f.save()
return redirect(request.POST['referer'])
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 1100000:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if(form.is_valid()):
file = request.FILES['file']
f = ProjectFile(project = project_api.get_project(projectID), file = file, name = file.name)
f.save()
return redirect(request.POST['referer'])
def upload(request):
# Handle file upload
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
if form.is_valid():
logger.debug('File with type ' +
request.FILES['docfile'].content_type + ' uploaded.')
if request.FILES[
'docfile'].content_type == u'application/vnd.oasis.opendocument.text':
file_name = saveFile(request.FILES['docfile'])
logger.info('Converting file ' + file_name)
content = subprocess.check_output([
'OdtConverter/odt2html', '-x', 'OdtConverter/odt2html.xsl',
'EditorApp/static/media/' + file_name
])
logger.info('Deleting file ' + file_name)
os.remove('EditorApp/static/media/' + file_name)
logger.info('Saving imported document ' + file_name)
create_document(None, file_name, content)
elif request.FILES['docfile'].content_type[:5] == u'image':
saveFile(request.FILES['docfile'])
else:
form = FileForm()
form.error = 'Invalid type of document.'
logger.error('Wrong type of document.')
return render(request, 'upload.html', {'form': form})
# Redirect to the document list after POST
return HttpResponseRedirect('/')
else:
form = FileForm() # A empty, unbound form
return render(request, 'upload.html', {'form': form})
def upload_file(request, upload_path=None, upload_link=None):
form = FileForm(request.POST, request.FILES)
if form.is_valid():
uploaded_file = form.cleaned_data['file']
file_name, extension = os.path.splitext(uploaded_file.name)
timestr = time.strftime(u"%Y%m%d-%H%M%S")
full_name = u'{0}{1}'.format(file_name+timestr, extension)
path = os.path.join(upload_path or UPLOAD_PATH, full_name)
image_path = default_storage.save(path, uploaded_file)
image_url = default_storage.url(image_path)
if upload_link:
return HttpResponse(image_url)
return HttpResponse(json.dumps({'filelink': image_url, 'filename': uploaded_file.name}))
return HttpResponseForbidden()
def home():
feature_form = FeatureForm()
file_form = FileForm()
with open ("static/final_svm_model.pkl",'rb') as pickle_file:
model = pickle.load(pickle_file)
if feature_form.validate_on_submit():
sepal_length= feature_form.sepal_length.data
sepal_width = feature_form.sepal_width.data
petal_length = feature_form.petal_length.data
petal_width = feature_form.petal_width.data
data = np.array([sepal_length,sepal_width, petal_length, petal_width]).reshape(1,-1)
prediction= model.predict(data)
predict_result = ""
if prediction == 0:
predict_result = 'setosa'
elif prediction == 1:
predict_result = 'versicolor'
else :
predict_result = 'virginica'
#image_file_name = str(uuid.uuid4())
#image_file = image_file_name + ".png"
#search_image(predict_result, image_file)
return render_template("home.html", feature_form=feature_form, file_form = file_form, result = predict_result)
elif file_form.validate_on_submit():
file = file_form.test_file.data #FileStorage object
try:
data= pd.read_csv(file,sep=' ', delimiter=r"\s+",index_col=False)
prediction = model.predict(data)
except Exception:
return "Something went worng. PLEASE CHECK THE FILE AGAIN"
prediction = prediction.astype(str)
prediction[prediction == '0'] = 'setosa'
prediction[prediction == '1'] = 'versicolor'
prediction[prediction == '2'] = 'virginica'
prediction_file_name = str(uuid.uuid4())
predict_result_file = prediction_file_name + ".txt"
np.savetxt("static/prediction/"+ predict_result_file, prediction, newline="\r\n" , fmt="%s")
return redirect(url_for('predict_txt', filename=predict_result_file))
return render_template("home.html", feature_form=feature_form, file_form = file_form)
def fsubmit():
error = None
form = FileForm(request.form)
if request.method == "POST":
print(form.validate())
print("file submitted : ", form.file)
print("name: ", request.files["file"])
# print("url submitted : " ,form.q.data)
print(request.files["file"].filename)
inp(request.files["file"].filename)
elif (request.method == "POST"):
error = "WRONG FILE!!!"
else:
return render_template("uploader.html", form=form)
return render_template("uploader.html", form=form, error=error)
def create(request):
# return render(request, 'files/create.html', {"foo": "bar"})
print 'entrou no create'
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
print 'request is post!'
print form.errors
if form.is_valid():
print 'form is valid!'
# print 'analysis name should be ', form.cleaned_data['name']
# file.name = form.cleaned_data['name']
file = File.objects.create(user=request.user)
file.file = request.FILES.get('file')
file.name = str(os.path.splitext(file.file.name)[0])
file.user = request.user
file.save()
f = file.file
#fix permissions
#os.chmod("%s/genomes/%s/" % (settings.BASE_DIR, fastafile.user), 0777)
# os.chmod("%s/uploads/%s/%s" % (settings.BASE_DIR, fastafile.user, fastafile.id), 0777)
#Align.delay(analysis.id)
data = {
'files': [{
'deleteType': 'DELETE',
'name': file.name,
'url': '',
'thumbnailUrl': '',
'type': 'image/png',
'deleteUrl': '',
'size': f.size
}]
}
response = JSONResponse(data, mimetype=response_mimetype(request))
response['Content-Disposition'] = 'inline; filename=files.json'
return response
else:
form = FileForm()
return render(request, 'files/create.html', {'form': form})
def files():
result = []
form = FileForm()
files = File.query.all()
for file in files:
result.append([file.file_name, file.file_link])
return render_template('files.html', rows=result, form=form)
def add_containt(request):
if request.user.is_authenticated():
args = {}
if request.POST:
try:
request.POST['file_field']
file_form = FileForm(request.POST, request.FILES)
if file_form.is_valid():
file_name = request.FILES['file']
media_containt = Media_containt(file=file_name)
media_containt.save()
pdf_file_name = str(file_name).replace(' ', '_')
image_file_name = str(file_name).replace(' ', '_').split('.')
image_file_name[-1] = 'png'
image_file_name = '.'.join(image_file_name)
cmd = 'gs -o '+media_files_url+image_file_name+' -sDEVICE=pngalpha -dLastPage=1 '+media_files_url+pdf_file_name
print cmd
subprocess.call(cmd, shell=True)
print 'save and redirect'
return HttpResponseRedirect('/elab/add/containt/')
else:
containt_form = ContaintForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print file_form.errors
return render_to_response('html_template/admin_template/admin_pannel.html', args)
except Exception, e:
print "Exception-->", e
containt_form = ContaintForm(request.POST)
if containt_form.is_valid():
containt_form.save()
return HttpResponseRedirect('/elab/add/containt/')
else:
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print containt_form.errors
return render_to_response('html_template/admin_template/admin_pannel.html', args)
else:
containt_form = ContaintForm()
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
return render_to_response('html_template/admin_template/admin_pannel.html', args)
def list_files(rctx):
dir_ = os.path.join(rctx.conf.MEDIA, 'stored')
if not os.path.isdir(dir_):
os.makedirs(dir_)
files = os.listdir(dir_)
form = FileForm({})
ui = HtmlUI(from_fields=True, engine=rctx.vals.jinja_env)
return dict(files=files, url='/media/stored/', form=form, ui=ui)
def post_file(env, data):
dir_ = prepair_dir(env)
files = os.listdir(dir_)
form = FileForm(env)
if form.accept(env.request.POST):
tmp_file = form.python_data['file']
if tmp_file is not None:
new_path = os.path.join(dir_, tmp_file.file_name)
os.rename(tmp_file.path, new_path)
raise HTTPSeeOther(location=env.request.url)
return env.template.render_to_response('index', {
'files':files,
'url':'/media/stored/',
'form':form
})
def post_file(env, data):
dir_ = prepair_dir(env)
files = os.listdir(dir_)
form = FileForm(env)
if form.accept(env.request.POST):
tmp_file = form.python_data['file']
if tmp_file is not None:
new_path = os.path.join(dir_, tmp_file.file_name)
os.rename(tmp_file.path, new_path)
raise HTTPSeeOther(location=env.request.url)
return env.template.render_to_response('index', {
'files': files,
'url': '/media/stored/',
'form': form
})
def insert_file():
form = FileForm()
name = form.name.data
link = form.link.data
file = File(file_name=name, file_link=link)
db.session.add(file)
db.session.commit()
return redirect('/file')
def attach_file(request,content_type_id,pk):
ct = ContentType.objects.get(id=content_type_id)
klass = ct.model_class()
obj = klass.objects.get(pk=pk)
if request.method == 'GET':
form = FileForm()
elif request.method == 'POST':
form = FileForm(request.POST,request.FILES)
if form.is_valid():
obj = form.save(commit=False)
obj.uploaded_by=request.user
obj.object_id = pk
obj.content_type = ct
obj.name = obj.file.name
obj.save()
return Response(FileSerializer(obj).data)
else:
return Response({'errors':form.errors},status=404)
def list_files(env, data):
dir_ = prepair_dir(env)
files = os.listdir(dir_)
form = FileForm(env)
return env.template.render_to_response('index', {
'files': files,
'url': '/media/stored/',
'form': form
})
def get_attachments(request, projectID):
form = FileForm()
context = {
'form': form,
'projectID': projectID,
'referer': request.META['HTTP_REFERER'],
'modalID': 'projAttachModal',
'files': ProjectFile.objects.filter(project__id=projectID)
}
return render(request, 'Attachments.html', context)
def my_bookmark(request, template_name='bookmark/my_bookmark.html'):
form = BookmarkForm()
file_form = FileForm()
return render_to_response(
template_name,
RequestContext(request, {
'form': form,
'file_form': file_form,
'active': 'my_bookmark'
}))
def batch_import_bulletin_by_excel(request):
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
if form.is_valid():
if request.FILES['filefield'].name.split('.')[-1] == 'xlsx':
try:
utils.handle_uploaded_file(request, f=request.FILES['filefield'])
except ObjectDoesNotExist, e:
error_message = '科室和医生组合不存在，请检查所上传表格内容后重新上传'
return render(request, 'publisher/file.html',
{'form': form, 'error_message': error_message,
'loginname': request.session['loginname']})
return render(request, 'publisher/file.html',
{'form': form, 'error_message': '上传成功！',
'loginname': request.session['loginname']})
else:
error_message = '文件格式错误，请上传Excel文件（.xlsl)'
form = FileForm()
return render(request, 'publisher/file.html', {'form': form, 'error_message': error_message, 'loginname': request.session['loginname']})
def upload_gl(request):
if request.method != "POST":
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
context = {'file_category': 'GL Projections'}
context['file_type'] = '.json'
context['obj_label'] = forecast_obj.label
form = FileForm()
context['form'] = form
return render_to_response('forecasts/upload_gl.html', RequestContext(request, context))
else:
form = FileForm(request.POST, request.FILES)
if form.is_valid():
upload = request.FILES.values()[0]
file_name = upload._name
data = json.loads(upload.file.read())
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
forecast_obj.projections = data
forecast_obj.save()
return HttpResponseRedirect('/forecasts/forecast/%s' % forecast_obj.id)
def file_edit(id):
fileobj = g.db.files.find_one({'_id': id})
if fileobj is None:
abort(404)
if fileobj.get('owner') != g.username or not (g.is_admin):
# abort if owner doesn't match current user or current is not admin
abort(403)
form = FileForm()
if form.validate_on_submit():
fileobj = form2object(form, fileobj)
flash('not implemented', category="warning")
if request.method == 'GET':
# get the data from the page-object into the form
form = object2form(fileobj, form)
return render_template('generic_form.html', form=form, title='Edit File')
def upload_file(request, **config):
file_type = config['file_type']
context = {'file_type': file_type,}
form = FileForm(request.POST, request.FILES)
if form.is_valid():
upload = request.FILES.values()[0]
file_name = upload._name
file_name_with_timestamp = save_file(upload)
company = utils.get_company(request)
model = config.pop('model')
unique = config.pop('unique')
name_cleaner_path = config.pop('name_cleaner')
value_cleaner_path = config.pop('value_cleaner')
exclude_path = config.pop('exclude')
post_process_path = config.pop('post_process')
#result is zero if it was able to start the background task successfully.
result, out, err = process_incoming_file(model, unique, name_cleaner, value_cleaner, exclude, post_process,
file_type=config['file_type'],
file_name=file_name_with_timestamp,
company=company,
task_title="%s data for %s" % (file_type, company),
task_success_url=reverse('upload_complete'),
)
if result != 0:
context.update({'file_name': file_name, 'success': False, 'out': out, 'err': err})
messages.error(request, 'Could not process the file provided, please see below')
return render(request, 'uploaded.html', context)
else:
return HttpResponseRedirect(reverse('task_result', kwargs={'pid':out,}))
else:
context.update({'file_name': file_name, 'success': False, 'out': out, 'err': err})
messages.error(request, 'Could not process the file provided, please see below')
return render(request, 'uploaded.html', context)
def teacher_resource(id):
course = Course.query.get(id)
resources = course.resources.all()
form = FileForm()
#：如果当前登录的教师没有教授这门课程，则禁止访问
if current_user.id != course.teacher.id:
abort(403)
if form.validate_on_submit():
name = form.file.data.filename
addr = 'upload/' + str(id) + '/' + 'resource/'
url = upload(
form.file.data,
['zip', 'rar', 'doc', 'txt', 'docx', 'pdf', 'ppt', 'pptx'], addr)
if url is None:
flash(
u'请选择正确的文件格式上传文件，文件格式可以是["zip", "rar", "doc", "txt", "docx", "pdf", "ppt", "pptx"]'
)
return render_template('teacherResource.html',
form=form,
course=course,
resources=resources)
resource = Resource.query.filter(
and_(Resource.course_id == id, Resource.name == name)).first()
#：如果是同名文件，则覆盖，即删除原文件，保留新文件
if resource is not None:
#：删除原文件
if os.path.exists(resource.url):
os.remove(resource.url)
resource.url = url
db.session.commit()
else:
resource = Resource(name=name, url=url, course_id=id)
db.session.add(resource)
db.session.commit()
flash(u'文件上传成功')
return redirect(url_for('teacher_resource', id=id))
return render_template('teacherResource.html',
form=form,
course=course,
resources=resources)
def file_upload_typed(request, folder_id=None, response_format='html'):
"File upload to preselected folder"
folder = None
if folder_id:
folder = get_object_or_404(Folder, pk=folder_id)
if not request.user.profile.has_permission(folder, mode='x'):
folder = None
if request.POST:
if 'cancel' not in request.POST:
form = FileForm(
request.user.profile, folder_id, request.POST, request.FILES)
if form.is_valid():
file = form.save()
file.set_user_from_request(request)
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
return HttpResponseRedirect(reverse('document_index'))
else:
form = FileForm(request.user.profile, folder_id)
context = _get_default_context(request)
context.update({'form': form,
'folder': folder})
return render_to_response('documents/file_upload_typed', context,
context_instance=RequestContext(request),
response_format=response_format)
def file_edit(request, file_id, response_format='html'):
"File edit page"
file = get_object_or_404(File, pk=file_id)
if not request.user.profile.has_permission(file, mode='w'):
return user_denied(request, message="You don't have access to this File")
if request.POST:
if 'cancel' not in request.POST:
form = FileForm(
request.user.profile, None, request.POST, request.FILES, instance=file)
if form.is_valid():
file = form.save()
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
form = FileForm(request.user.profile, None, instance=file)
context = _get_default_context(request)
context.update({'form': form,
'file': file})
return render_to_response('documents/file_edit', context,
context_instance=RequestContext(request),
response_format=response_format)
def create(request):
# return render(request, 'files/create.html', {"foo": "bar"})
print 'entrou no create'
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
print 'request is post!'
print form.errors
if form.is_valid():
print 'form is valid!'
# print 'analysis name should be ', form.cleaned_data['name']
# file.name = form.cleaned_data['name']
file = File.objects.create(user=request.user)
file.file= request.FILES.get('file')
file.name= str(os.path.splitext(file.file.name)[0])
file.user = request.user
file.save()
f = file.file
#fix permissions
#os.chmod("%s/genomes/%s/" % (settings.BASE_DIR, fastafile.user), 0777)
# os.chmod("%s/uploads/%s/%s" % (settings.BASE_DIR, fastafile.user, fastafile.id), 0777)
#Align.delay(analysis.id)
data = {'files': [{'deleteType': 'DELETE', 'name': file.name, 'url': '', 'thumbnailUrl': '', 'type': 'image/png', 'deleteUrl': '', 'size': f.size}]}
response = JSONResponse(data, mimetype=response_mimetype(request))
response['Content-Disposition'] = 'inline; filename=files.json'
return response
else:
form = FileForm()
return render(request, 'files/create.html', {'form':form})
def upload_gl(request):
if request.method != "POST":
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
context = {'file_category': 'GL Projections'}
context['file_type'] = '.json'
context['obj_label'] = forecast_obj.label
form = FileForm()
context['form'] = form
return render_to_response('forecasts/upload_gl.html',
RequestContext(request, context))
else:
form = FileForm(request.POST, request.FILES)
if form.is_valid():
upload = request.FILES.values()[0]
file_name = upload._name
data = json.loads(upload.file.read())
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
forecast_obj.projections = data
forecast_obj.save()
return HttpResponseRedirect('/forecasts/forecast/%s' %
forecast_obj.id)
def import_bookmark(request, template_name='bookmark/import_bookmark.html'):
file_form = FileForm(request.POST or None, request.FILES or None)
if request.method == 'POST' and file_form.is_valid():
file = request.FILES['file']
tags_input = file_form.cleaned_data['tags']
public =file_form.cleaned_data['public']
try:
bookmarks = parse_firefox_bookmark(file)
for bk in bookmarks:
try:
bookmark = Bookmark.objects.create(url=bk['url'], title=bk['title'], owner=request.user, public=public)
if tags_input:
tags = tags_input
else:
tags=parse_tags(bk['tags'])
for tag in tags:
bookmark.tags.add(tag)
# Update the screen shot
update_bk_screen_shot_async(bookmark)
except Exception:
pass
return HttpResponseRedirect(reverse("my_bookmark"))
except Exception, e:
file_form._errors[NON_FIELD_ERRORS] = ErrorList([e.message])
def add_containt(request):
if request.user.is_authenticated():
args = {}
if request.POST:
try:
request.POST['file_field']
file_form = FileForm(request.POST, request.FILES)
if file_form.is_valid():
file_name = request.FILES['file']
media_containt = Media_containt(file=file_name)
media_containt.save()
pdf_file_name = str(file_name).replace(' ', '_')
image_file_name = str(file_name).replace(' ',
'_').split('.')
image_file_name[-1] = 'png'
image_file_name = '.'.join(image_file_name)
cmd = 'gs -o ' + media_files_url + image_file_name + ' -sDEVICE=pngalpha -dLastPage=1 ' + media_files_url + pdf_file_name
print cmd
subprocess.call(cmd, shell=True)
print 'save and redirect'
return HttpResponseRedirect('/elab/add/containt/')
else:
containt_form = ContaintForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print file_form.errors
return render_to_response(
'html_template/admin_template/admin_pannel.html', args)
except Exception, e:
print "Exception-->", e
containt_form = ContaintForm(request.POST)
if containt_form.is_valid():
containt_form.save()
return HttpResponseRedirect('/elab/add/containt/')
else:
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print containt_form.errors
return render_to_response(
'html_template/admin_template/admin_pannel.html', args)
else:
containt_form = ContaintForm()
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
return render_to_response(
'html_template/admin_template/admin_pannel.html', args)
def batch_import_bulletin_by_excel(request):
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
if form.is_valid():
if request.FILES['filefield'].name.split('.')[-1] == 'xlsx':
utils.handle_uploaded_file(request,
f=request.FILES['filefield'])
return render(request, 'publisher/file.html', {
'form': form,
'error_message': '上传成功！'
})
else:
error_message = '文件格式错误，请上传Excel文件（.xlsl)'
form = FileForm()
return render(request, 'publisher/file.html', {
'form': form,
'error_message': error_message
})
else:
form = FileForm()
return render(request, 'publisher/file.html', {'form': form})
def file_upload(request, response_format='html'):
"New file form"
if request.POST:
if 'cancel' not in request.POST:
file = File()
form = FileForm(
request.user.profile, None, request.POST, request.FILES, instance=file)
if form.is_valid():
file = form.save()
file.set_user_from_request(request)
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
return HttpResponseRedirect(reverse('document_index'))
else:
form = FileForm(request.user.profile, None)
context = _get_default_context(request)
context.update({'form': form})
return render_to_response('documents/file_upload', context,
context_instance=RequestContext(request),
response_format=response_format)
def file_form(request):
# if not request.user.is_staff or not request.user.is_superuser:
# raise Http404;
if request.POST:
form = FileForm(request.POST, request.FILES)
if form.is_valid():
instance = form.save(commit=False)
instance.user = request.user
instance.save()
# read CSV file and define parameters
input_file_name = re.search(r'/(media/.*)', instance.file.url)
fileID = instance.id
input_file = vcf.Reader(open(input_file_name.group(1), "r"))
# output_somatic_file = open('media/somatic_mutation-'+str(fileID)+'.tsv', 'wb')
# output_germline_file = open('media/germline_mutation-'+str(fileID)+'.tsv', 'wb')
logs = open('media/logs-'+str(fileID)+'.txt', 'w')
somatic_mutation_array = []
germline_mutation_array = []
# Read vcf file and create seperate arrays for somatic and germline mutation
for record in input_file:
chr = re.search(r'chr(.*)', str(record.CHROM))
start_pos = str(record.POS)
if record.REF == '-':
end_pos = record.POS + 1
else:
end_pos = start_pos
ref = str(record.REF)
alt = re.search(r'\[(.*)\]', str(record.ALT))
oncoTator = 'http://www.broadinstitute.org/oncotator/mutation/' + chr.group(
1) + '_' + start_pos + '_' + end_pos + '_' + ref + '_' + alt.group(1)
try:
oncoTator_response = requests.get(oncoTator)
except ConnectionError as e:
print e
logs.write(str(e))
oncoTator_response = "No response"
if oncoTator_response != "No response" and oncoTator_response.status_code != 500:
mutation = json.loads(oncoTator_response.text)
if "ERROR" in mutation:
logs.write("OncoTator is giving error for url:" + oncoTator + " Error message: " + str(oncoTator_response.text))
else:
if mutation["CGC_Cancer Germline Mut"] == "yes":
germline_mutation_array.append(mutation)
if mutation["CGC_Cancer Somatic Mut"] == "yes":
somatic_mutation_array.append(mutation)
logs.close()
# write values from arrays to tsv files
# fieldnames = []
# for key in somatic_mutation_array[0]:
# fieldnames.append(str(key))
# tsv_somatic_file = csv.DictWriter(output_somatic_file, fieldnames=fieldnames, delimiter='\t')
# tsv_somatic_file.writeheader()
for mutation in somatic_mutation_array:
# tsv_somatic_file.writerow(mutation)
ssnp = somatic_snp.objects.create(study_name=instance, gene=mutation["gene"], chromosome=mutation["ESP_Chromosome"], start=mutation["start"], end=mutation["end"], ref_allele=mutation["ref_allele"], alt_allele=mutation["alt_allele"], variant_class=mutation["variant_classification"],variant_type=mutation["variant_type"], ensemblID=mutation["HGNC_Ensembl Gene ID"])
# output_somatic_file.close()
# tsv_germline_file = csv.DictWriter(output_germline_file, fieldnames=fieldnames, delimiter='\t')
# tsv_germline_file.writeheader()
for mutation in germline_mutation_array:
# tsv_germline_file.writerow(mutation)
gsnp = germline_snp.objects.create(study_name=instance, gene=mutation["gene"], chromosome=mutation["ESP_Chromosome"], start=mutation["start"], end=mutation["end"], ref_allele=mutation["ref_allele"], alt_allele=mutation["alt_allele"], variant_class=mutation["variant_classification"],variant_type=mutation["variant_type"], ensemblID=mutation["HGNC_Ensembl Gene ID"])
# output_germline_file.close()
# fileread = open('media/germline_mutation-'+str(fileID)+'.tsv', 'r')
# TSVfile = File(fileread)
# instance.germline_result.save('media/germline_mutation-'+str(fileID)+'.tsv', TSVfile, save=True)
#
# fileread = open('media/somatic_mutation-' + str(fileID) + '.tsv', 'r')
# TSVfile = File(fileread)
# instance.somatic_result.save('media/somtic_mutation-' + str(fileID) + '.tsv', TSVfile, save=True)
return HttpResponseRedirect('/result/')
else:
form = FileForm()
return render(request, 'oncotator/snp_tools.html', {'form': form})
