def genome_uploader(request):
if request.user.is_authenticated():
if request.user.is_staff == True:
if request.POST.has_key("species") and request.POST.has_key("genbank_id"):
organism_name = request.POST["species"]
genbank_id = request.POST["genbank_id"]
if request.FILES.has_key("genbank_file"):
uploaded_file = request.FILES["genbank_file"]
genbank_file = GenomeUpload(genbank_file=uploaded_file, name=uploaded_file.name)
genbank_file.save()
try:
organism_exists = True
organism = Organism.objects.get(species=organism_name)
except ObjectDoesNotExist:
organism_exists = False
next_id = Organism.objects.order_by("-organism_id")[0].organism_id + 1
organism = Organism(
organism_id=next_id,
abbreviation="M. " + organism_name,
genus="Mycoplasma",
species=organism_name,
common_name="Mycoplasma " + organism_name,
)
organism.save()
landmark = Landmark(name=genbank_id, organism_id=organism.organism_id)
landmark.save()
error = process_genome_file(genbank_file, organism, genbank_id, request, organism_exists)
if error[0]:
error_code = "0"
landmark.delete()
organism.delete()
else:
error_code = "1"
error_msg = error_code + "," + str(error[1])
return HttpResponse(error_msg)
else:
return HttpResponse("-1")
else:
return HttpResponse("0")
else:
return HttpResponseRedirect(reverse("mycoplasma_home.views.home"))
else:
return HttpResponseRedirect(reverse("mycoplasma_home.views.home"))
def genome_uploader(request):
if (request.user.is_authenticated()):
if (request.user.is_staff == True):
if (request.POST.has_key('species')
and request.POST.has_key('genbank_id')):
organism_name = request.POST['species']
genbank_id = request.POST['genbank_id']
if (request.FILES.has_key('genbank_file')):
uploaded_file = request.FILES['genbank_file']
genbank_file = GenomeUpload(genbank_file=uploaded_file,
name=uploaded_file.name)
genbank_file.save()
try:
organism_exists = True
organism = Organism.objects.get(species=organism_name)
except ObjectDoesNotExist:
organism_exists = False
next_id = Organism.objects.order_by(
'-organism_id')[0].organism_id + 1
organism = Organism(organism_id=next_id,
abbreviation="M. " + organism_name,
genus="Mycoplasma",
species=organism_name,
common_name="Mycoplasma " +
organism_name)
organism.save()
landmark = Landmark(name=genbank_id,
organism_id=organism.organism_id)
landmark.save()
error = process_genome_file(genbank_file, organism,
genbank_id, request,
organism_exists)
if error[0]:
error_code = '0'
landmark.delete()
organism.delete()
else:
error_code = '1'
error_msg = error_code + "," + str(error[1])
return HttpResponse(error_msg)
else:
return HttpResponse('-1')
else:
return HttpResponse('0')
else:
return HttpResponseRedirect(reverse('mycoplasma_home.views.home'))
else:
return HttpResponseRedirect(reverse('mycoplasma_home.views.home'))
def process_genome_file(genbank_file, organism, genbank_id, request,
organism_exists):
error = (False, "", 0)
if (request.session.get(organism.species, None) == None):
request.session[organism.species] = '0'
session_index = 0
session_array = ['0']
else:
request.session[organism] = request.session[organism.species] + ',0'
session_index = len(request.session[organism.species].split(',')) - 1
session_array = request.session[organism.species].split(',')
static_root_absolute = settings.STATICFILES_DIRS[0]
media_root_absolute = settings.MEDIA_ROOT + "/genbank_files/"
extension_place = genbank_file.name.rfind(".")
file_extension = genbank_file.name[extension_place + 1:]
gff_name = media_root_absolute + genbank_file.name
if (file_extension == "gbk"):
args = [
"bp_genbank2gff3.pl", "-noCDS",
media_root_absolute + genbank_file.name, "--outdir",
media_root_absolute
]
error = run_subproc(args, 0, request, session_array, session_index,
organism)
gff_name = media_root_absolute + genbank_file.name + ".gff"
# remove the genbank file to deal with the gff only
os.system("rm " + media_root_absolute + genbank_file.name)
genbank_file.delete()
elif (file_extension == "gff"):
gff_name = media_root_absolute + genbank_file.name
genbank_file.delete()
else:
error = (
True,
"Please enter a genbank or gff file with the extension .gff or .gbk",
0)
gff_name = media_root_absolute + genbank_file.name
'''
if (not error[0]):
if(os.getenv("GMOD_ROOT") == None):
os.putenv("GMOD_ROOT", "/usr/local/gmod/")
args = ["gmod_gff3_preprocessor.pl","--outfile", gff_name, "--gfffile", gff_name]
error = run_subproc(args, 2, request, session_array, session_index, organism.species)
'''
if (not error[0]):
'''args = ["python", static_root_absolute + "/python_scripts/prepGFFGO.py", "--file", gff_name, "--outfile",
gff_name + ".sorted.colored", "--accession", genbank_id]
error = run_subproc(args, 3, request, session_array, session_index, organism.species)
'''
gffRewriter = GFFRewriter(filename=gff_name,
outfile=gff_name + ".sorted.prepared",
accession=genbank_id)
gffRewriter.addUnknownCvTerms({
'user':
settings.DATABASES['chado']['USER'],
'password':
settings.DATABASES['chado']['PASSWORD'],
'db':
settings.DATABASES['chado']['NAME']
})
gffRewriter.addColor({
'user':
settings.DATABASES['chado']['USER'],
'password':
settings.DATABASES['chado']['PASSWORD'],
'db':
'MyGO'
})
error = gffRewriter.getError(3)
if (not error[0]):
organism_name = organism.species
# need to upload to a temporary organism to maintain database integrity
if (organism_exists):
organism_name += "_temp"
next_id = Organism.objects.order_by(
'-organism_id')[0].organism_id + 1
temp_organism = Organism(organism_id=next_id,
abbreviation="M. " + organism_name,
genus="Mycoplasma",
species=organism_name,
common_name="Mycoplasma " + organism_name)
temp_organism.save()
args = [
"gmod_bulk_load_gff3.pl", "--organism",
"Mycoplasma " + organism_name, "--gfffile",
gff_name + ".sorted.prepared", "--dbname",
settings.DATABASES['chado']['NAME'], "--dbuser",
settings.DATABASES['chado']['USER'], "--dbpass",
settings.DATABASES['chado']['PASSWORD'], "--random_tmp_dir"
]
error = run_subproc(args, 4, request, session_array, session_index,
organism.species)
if (not error[0] and organism_exists):
# since there was no error in the upload, we remove the old organism and accept the new organism
replace_name = organism.species
organism.delete()
temp_organism.update(species=replace_name)
temp_organism.save()
# the gff file should be deleted no matter what
#os.system("rm " + gff_name)
#os.system("rm " + gff_name + ".sorted")
#os.system("rm " + gff_name + ".sorted.fasta")
#os.system("rm " + gff_name + ".sorted.colored")
# set the status of the upload process to 5
session_array[session_index] = '5'
request.session[organism.species] = ",".join(session_array)
if (not error[0]):
if (not organism_exists):
error = create_new_gbrowse_entry(organism.species, genbank_id)
# set the status of the upload process to 6
session_array[session_index] = '6'
request.session[organism.species] = ",".join(session_array)
return error
def process_genome_file(genbank_file, organism, genbank_id, request, organism_exists):
error = (False, "", 0)
if request.session.get(organism.species, None) == None:
request.session[organism.species] = "0"
session_index = 0
session_array = ["0"]
else:
request.session[organism] = request.session[organism.species] + ",0"
session_index = len(request.session[organism.species].split(",")) - 1
session_array = request.session[organism.species].split(",")
static_root_absolute = settings.STATICFILES_DIRS[0]
media_root_absolute = settings.MEDIA_ROOT + "/genbank_files/"
extension_place = genbank_file.name.rfind(".")
file_extension = genbank_file.name[extension_place + 1 :]
gff_name = media_root_absolute + genbank_file.name
if file_extension == "gbk":
args = [
"bp_genbank2gff3.pl",
"-noCDS",
media_root_absolute + genbank_file.name,
"--outdir",
media_root_absolute,
]
error = run_subproc(args, 0, request, session_array, session_index, organism)
gff_name = media_root_absolute + genbank_file.name + ".gff"
# remove the genbank file to deal with the gff only
os.system("rm " + media_root_absolute + genbank_file.name)
genbank_file.delete()
elif file_extension == "gff":
gff_name = media_root_absolute + genbank_file.name
genbank_file.delete()
else:
error = (True, "Please enter a genbank or gff file with the extension .gff or .gbk", 0)
gff_name = media_root_absolute + genbank_file.name
"""
if (not error[0]):
if(os.getenv("GMOD_ROOT") == None):
os.putenv("GMOD_ROOT", "/usr/local/gmod/")
args = ["gmod_gff3_preprocessor.pl","--outfile", gff_name, "--gfffile", gff_name]
error = run_subproc(args, 2, request, session_array, session_index, organism.species)
"""
if not error[0]:
"""args = ["python", static_root_absolute + "/python_scripts/prepGFFGO.py", "--file", gff_name, "--outfile",
gff_name + ".sorted.colored", "--accession", genbank_id]
error = run_subproc(args, 3, request, session_array, session_index, organism.species)
"""
gffRewriter = GFFRewriter(filename=gff_name, outfile=gff_name + ".sorted.prepared", accession=genbank_id)
gffRewriter.addUnknownCvTerms(
{
"user": settings.DATABASES["chado"]["USER"],
"password": settings.DATABASES["chado"]["PASSWORD"],
"db": settings.DATABASES["chado"]["NAME"],
}
)
gffRewriter.addColor(
{
"user": settings.DATABASES["chado"]["USER"],
"password": settings.DATABASES["chado"]["PASSWORD"],
"db": "MyGO",
}
)
error = gffRewriter.getError(3)
if not error[0]:
organism_name = organism.species
# need to upload to a temporary organism to maintain database integrity
if organism_exists:
organism_name += "_temp"
next_id = Organism.objects.order_by("-organism_id")[0].organism_id + 1
temp_organism = Organism(
organism_id=next_id,
abbreviation="M. " + organism_name,
genus="Mycoplasma",
species=organism_name,
common_name="Mycoplasma " + organism_name,
)
temp_organism.save()
args = [
"gmod_bulk_load_gff3.pl",
"--organism",
"Mycoplasma " + organism_name,
"--gfffile",
gff_name + ".sorted.prepared",
"--dbname",
settings.DATABASES["chado"]["NAME"],
"--dbuser",
settings.DATABASES["chado"]["USER"],
"--dbpass",
settings.DATABASES["chado"]["PASSWORD"],
"--random_tmp_dir",
]
error = run_subproc(args, 4, request, session_array, session_index, organism.species)
if not error[0] and organism_exists:
# since there was no error in the upload, we remove the old organism and accept the new organism
replace_name = organism.species
organism.delete()
temp_organism.update(species=replace_name)
temp_organism.save()
# the gff file should be deleted no matter what
# os.system("rm " + gff_name)
# os.system("rm " + gff_name + ".sorted")
# os.system("rm " + gff_name + ".sorted.fasta")
# os.system("rm " + gff_name + ".sorted.colored")
# set the status of the upload process to 5
session_array[session_index] = "5"
request.session[organism.species] = ",".join(session_array)
if not error[0]:
if not organism_exists:
error = create_new_gbrowse_entry(organism.species, genbank_id)
# set the status of the upload process to 6
session_array[session_index] = "6"
request.session[organism.species] = ",".join(session_array)
return error
