def write_plupload(request, pub_name):
"""file upload for plupload"""
logger.info("Starting write plupload")
pub = models.Publisher.objects.get(name=pub_name)
logger.debug("%s %s" %
(str(type(request.REQUEST['meta'])), request.REQUEST['meta']))
logger.debug("Publisher Plupload started")
if request.method == 'POST':
name = request.REQUEST.get('name', '')
uploaded_file = request.FILES['file']
if not name:
name = uploaded_file.name
logger.debug("plupload name = '%s'" % name)
#check to see if a user has uploaded a file before, and if they have
#not, make them a upload directory
upload_dir = "/results/referenceLibrary/temp"
if not os.path.exists(upload_dir):
return render_to_json({"error": "upload path does not exist"})
dest_path = os.path.join(upload_dir, name)
logger.debug("plupload destination = '%s'" % dest_path)
chunk = request.REQUEST.get('chunk', '0')
chunks = request.REQUEST.get('chunks', '0')
logger.debug("plupload chunk %s %s of %s" %
(str(type(chunk)), str(chunk), str(chunks)))
debug = [chunk, chunks]
with open(dest_path, ('wb' if chunk == '0' else 'ab')) as f:
for content in uploaded_file.chunks():
logger.debug("content chunk = '%d'" % len(content))
f.write(content)
if int(chunk) + 1 >= int(chunks):
try:
upload = move_upload(pub, dest_path, name,
request.REQUEST['meta'])
async_upload = run_pub_scripts.delay(pub, upload)
except Exception as err:
logger.exception(
"There was a problem during upload of a file for a publisher."
)
else:
logger.info("Successfully pluploaded %s" % name)
logger.debug("plupload done")
return render_to_json({"chunk posted": debug})
else:
return render_to_json({"method": "only post here"})
def write_plupload(request, pub_name):
"""file upload for plupload"""
logger.info("Starting write plupload")
pub = models.Publisher.objects.get(name=pub_name)
logger.debug("%s %s" % (str(type(request.REQUEST['meta'])), request.REQUEST['meta']))
logger.debug("Publisher Plupload started")
if request.method == 'POST':
name = request.REQUEST.get('name','')
uploaded_file = request.FILES['file']
if not name:
name = uploaded_file.name
logger.debug("plupload name = '%s'" % name)
#check to see if a user has uploaded a file before, and if they have
#not, make them a upload directory
upload_dir = "/results/referenceLibrary/temp"
if not os.path.exists(upload_dir):
return render_to_json({"error":"upload path does not exist"})
dest_path = os.path.join(upload_dir, name)
logger.debug("plupload destination = '%s'" % dest_path)
chunk = request.REQUEST.get('chunk','0')
chunks = request.REQUEST.get('chunks','0')
logger.debug("plupload chunk %s %s of %s" % (str(type(chunk)), str(chunk), str(chunks)))
debug = [chunk, chunks]
with open(dest_path,('wb' if chunk=='0' else 'ab')) as f:
for content in uploaded_file.chunks():
logger.debug("content chunk = '%d'" % len(content))
f.write(content)
my_contentupload_id = None
if int(chunk) + 1 >= int(chunks):
try:
upload = move_upload(pub, dest_path, name, request.REQUEST['meta'])
async_upload = run_pub_scripts.delay(pub, upload)
my_contentupload_id = upload.id
except Exception as err:
logger.exception("There was a problem during upload of a file for a publisher.")
else:
logger.info("Successfully pluploaded %s" % name)
logger.debug("plupload done")
return render_to_json({"chunk posted": debug, "contentupload_id": my_contentupload_id})
else:
return render_to_json({"method":"only post here"})
def delete_genome(request, pk):
"""delete a reference genome
the filesystem file deletions should be done with a method on the model"""
if request.method=="POST":
rg = shortcuts.get_object_or_404(models.ReferenceGenome, pk=pk)
with_dir = request.GET.get('with_dir', False)
#delete dir by default
try_delete = rg.delete()
if not try_delete:
#the file could not be deleted, present the user with an error message.
return render_to_json({"status":" <strong>Error</strong> <p>Genome could not be deleted.</p> \
<p>Check the file permissions for the genome on the file system at: </p> \
<p><strong>" + str(rg.reference_path) + "</p></strong> "})
return render_to_json({"status":"Genome was deleted successfully"})
if request.method == "GET":
return render_to_json({"status":"This must be accessed via post"})
def genome_status(request, pk):
"""Provide a way for the index creator to let us know when the index has been created"""
if request.method=="POST":
rg = shortcuts.get_object_or_404(models.ReferenceGenome, pk=pk)
status = request.POST.get('status',False)
enabled = request.POST.get('enabled',False)
verbose_error = request.POST.get('verbose_error',"")
index_version = request.POST.get('index_version',"")
if not status:
return render_to_json({"status":"error genome status not given"})
rg.status = status
rg.enabled = enabled
rg.verbose_error = verbose_error
rg.index_version = index_version
rg.reference_path = os.path.join(settings.TMAP_DIR, rg.short_name)
rg.save()
return render_to_json({"status":"genome status updated", "enabled" : enabled })
if request.method=="GET":
rg = shortcuts.get_object_or_404(models.ReferenceGenome, pk=pk)
return render_to_json({"status":rg.status})
def fileUpload(request):
"""file upload for plupload"""
if request.method == 'POST':
name = request.REQUEST.get('name','')
uploaded_file = request.FILES['file']
if not name:
name = uploaded_file.name
name,ext = os.path.splitext(name)
#check to see if a user has uploaded a file before, and if they have
#not, make them a upload directory
upload_dir = "/results/referenceLibrary/temp/"
if not os.path.exists(upload_dir):
return render_to_json({"error":"upload path does not exist"})
dest_path = '%s%s%s%s' % (upload_dir,os.sep,name,ext)
chunk = request.REQUEST.get('chunk','0')
chunks = request.REQUEST.get('chunks','0')
debug = [chunk, chunks]
with open(dest_path,('wb' if chunk==0 else 'ab')) as f:
for content in uploaded_file.chunks():
f.write(content)
if int(chunk) + 1 >= int(chunks):
#the upload has finished
pass
return render_to_json({"chuck posted":debug})
else:
return render_to_json({"method":"only post here"})
def new_genome(request):
"""This is the page to create a new genome. The XML-RPC server is ionJobServer.
"""
if request.method=="POST":
"""parse the data sent in"""
#required
name = request.POST.get('name',False)
short_name = request.POST.get('short_name',False)
fasta = request.POST.get('target_file',False)
version = request.POST.get('version',False)
notes = request.POST.get('notes',"")
#optional
read_sample_size = request.POST.get('read_sample_size',False)
read_exclude_length = request.POST.get('read_exclude_length',False)
#URL download
url = request.POST.get('url',False)
#if any of those were false send back a failed message
if not all((name, short_name, fasta, version)):
return render_to_json({"status":"Form validation failed","error":True})
if not set(short_name).issubset("abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_"):
return render_to_json( {"status":"The short name has invalid characters. The valid values are letters, numbers, and underscores.","error": True} )
#TODO: check to make sure the zip file only has one fasta or fa
path = "/results/referenceLibrary/temp/"
if not url:
#check to ensure the size on the OS the same as the reported.
reported_file_size = request.POST.get('reported_file_size',False)
try:
uploaded_file_size = str(os.path.getsize(path + fasta))
except OSError:
return render_to_json( {"status":"The FASTA temporary files was not found","error":True} )
if reported_file_size != uploaded_file_size :
try:
os.remove(path + fasta)
pass
except OSError:
return render_to_json( {"status":"The FASTA temporary did not match the expected size, and could not be deleted.","error":True} )
return render_to_json( {"status":
"The file you uploaded differs from the expected size. This is due to an error uploading. The temporary file has been removed.",
"reported": reported_file_size,
"uploaded": uploaded_file_size,
"error" : True
} )
#Make an genome ref object
if models.ReferenceGenome.objects.filter(short_name=short_name,index_version=settings.TMAP_VERSION):
#check to see if the genome already exists in the database with the same version
return render_to_json({"status":"Failed - Genome with this short name and index version already exist.","error":True})
rg = models.ReferenceGenome()
rg.name = name
rg.short_name = short_name
rg.version = version
rg.date = datetime.datetime.now()
rg.notes = notes
rg.status = "queued"
rg.enabled = False
rg.index_version = settings.TMAP_VERSION
#before the object is saved we should ping the xml-rpc server to see if it is alive.
try:
host = "127.0.0.1"
conn = client.connect(host,settings.JOBSERVER_PORT)
#just check uptime to make sure the call does not fail
conn.uptime()
except (socket.error,xmlrpclib.Fault):
return render_to_json( {"status":"Unable to connect to ionJobserver process. You may need to restart ionJobserver","error":True} )
#if the above didn't fail then we can save the object
#this object must be saved before the tmap call is made
rg.save()
#kick off the anaserve tmap xmlrpc call
import traceback
try:
host = "127.0.0.1"
conn = client.connect(host,settings.JOBSERVER_PORT)
tmap_bool, tmap_status = conn.tmap(str(rg.id), fasta, short_name, name, version, read_sample_size, read_exclude_length, settings.TMAP_VERSION)
except (socket.error,xmlrpclib.Fault):
#delete the genome object, because it was not sucessful
rg.delete()
return render_to_json( {"status":"Error with index creation", "error" : traceback.format_exc() } )
if not tmap_bool:
rg.delete()
return render_to_json( {"status":tmap_status,"error":True} )
return render_to_json({"status":"The genome index is being created. This might take a while, check the status on the references tab. You are being redirected there now.","error":False})
elif request.method=="GET":
ctxd = {}
ctx = template.RequestContext(request, ctxd)
#when we get a POST that data should be validated and go to the xmlrpc process
return shortcuts.render_to_response("rundb/ion_new_genome.html", context_instance=ctx)