def run():
if currentProgram.getExecutableFormat() != ElfLoader.ELF_NAME:
popup('Not an ELF file, cannot continue')
return
arch = 'hppa'
abi = 'default'
Constants(currentProgram, currentSelection, monitor, state, arch, abi)
def run():
if currentProgram.getExecutableFormat() != ElfLoader.ELF_NAME:
popup('Not an ELF file, cannot continue')
return
arch = getDebianName()
if arch == None:
popup('Architecture not defined')
return
abi = 'default' if arch not in DEFAULT_ABIS else DEFAULT_ABIS[arch]
obj = Constants(currentProgram, currentSelection, monitor, state, arch, abi)
def index(request, sz_error = ""):
sz_error_file = ""
constants = Constants()
file_model = FileModel()
radioButtons = RadioButtons()
### set privacy options
if (request.session.has_key(Constants.TAG_SESSION_OPTION_SELECT)):
radioButtons.fields['choice_field'].initial = request.session[Constants.TAG_SESSION_OPTION_SELECT]
else: radioButtons.fields['choice_field'].initial = "2"
if (request.session.has_key(Constants.TAG_SESSION_EMAIL)):
file_model.email = request.session[Constants.TAG_SESSION_EMAIL]
### set info privacy
file_model.n_privacy_options_id = int(radioButtons.fields['choice_field'].initial) - 1
if (file_model.n_privacy_options_id == 1):
sz_info_privacy = Privacy.CHOICES[file_model.n_privacy_options_id][1]
else: sz_info_privacy = Privacy.CHOICES[file_model.n_privacy_options_id][1]
### replace information
if (sz_info_privacy.find("We keep your analysis and") == 0):
sz_info_privacy = sz_info_privacy.replace("We keep your analysis and", "By default, we keep your analysis and")
if (request.POST.has_key('example')):
file_model.sz_sequences = ">Species_1\n---AAAAAAAAAAAaaaaAAAAAAAAA\n"\
">Species_2\n---AAAAAAAAAAAaaaaAAAAAAAAG\n"\
">Species_3\nAAAAAAAAAAAAAAaaaaAAAAAaATg\n"\
">Species_4\nAAAAAAAAAAAAAAAAAAAAAAnaCTg\n"\
">Species_5\nAAAAAAAAAAAAAAAAAAAAAANUCTG\n"\
">Species_6\nAAAAAAAAAAAAAAAAAAAAAAAUCTG\n"
elif (request.POST.has_key('clean')):
file_model.sz_sequences = ""
elif (request.POST.has_key('submit') or request.POST.has_key('upload')): ### test if the data is fast and all lines has the same size
sz_file = ""
b_test = True
## https://docs.djangoproject.com/en/1.7/topics/http/file-uploads/
if (request.POST.has_key('upload')): ### by file
form = UploadFileForm(request.POST, request.FILES)
if form.is_valid():
file_model.file_name = str(request.FILES['file'])
sz_file = constants.get_file_name(Constants.PATH_TEMP, Constants.FILE_TAG_TEMP, "")
(b_test, sz_error_file) = constants.save_file_disk(sz_file, request.FILES['file'])
if (b_test): (b_test, sz_error_file) = constants.is_fasta(sz_file)
else:
sz_error_file = "Error: choose a FASTA file, please..."
b_test = False
else: ### sequence posted
sz_file = constants.get_file_name(Constants.PATH_TEMP, Constants.FILE_TAG_TEMP, "")
file_model.sz_sequences = request.POST['sequence'].replace(" ", "")
handle = open(sz_file, "w")
handle.write(file_model.sz_sequences)
handle.close()
## test fasta
(b_test, sz_error) = constants.is_fasta(sz_file)
if (b_test):
(b_test, sz_error, n_species, n_length_sequences) = constants.is_accept_more_species_length(sz_file)
if (b_test):
#### submit file to SGE
submit = clProcessSGE()
file_model_temp = FileModel()
## get a unique ID for the job...
n_count = 0
while 1:
(file_model.key_id, file_model.hash_id) = constants.get_key_and_hash(sz_file, file_model.hash_id)
n_count += 1
if (n_count > 10):
file_model.key_id = ""
break
sz_composed_key = "%s_%s" % (file_model.key_id, file_model.hash_id)
if (not file_model_temp.__class__.objects.filter(key_id=sz_composed_key).exists()):
file_model.key_id = sz_composed_key
break
## submit the job
if (len(file_model.key_id) > 0):
(b_fail, sz_error) = submit.submit_sge(sz_file, file_model, Constants.PATH_LVB_SGE_WORK_DIRECTORY)
if (not b_fail):
file_model.path_job = file_model.key_id
file_model.n_species = n_species
file_model.n_length_sequences = n_length_sequences
file_model.save()
request.session[Constants.TAG_SESSION_KEY_ID] = file_model.key_id
constants.remove_file(sz_file)
return HttpResponseRedirect(reverse('lvb:result', args=(file_model.key_id,)))
else:
sz_error = "Some problem with he server. Please, try again..."
constants.remove_file(sz_file)
else:
file_model.sz_sequences = ""
## to not reload the page
file_model.is_finished = True
return render(request, 'lvb/index.html', {'file_model': file_model, 'radioButtons': radioButtons,
'lvb': "xpto", 'error_message': sz_error, 'error_message_file': sz_error_file,
'sz_info_privacy' : sz_info_privacy} )
def result(request, key_id):
## send email
if (request.POST.has_key('sendEmailData')):
return send_email(request, key_id, request.POST['sendEmailData'])
is_reload_page = False
constants = Constants()
file_model_temp = FileModel()
key_id = key_id.strip()
query_set = file_model_temp.__class__.objects.filter(key_id=key_id)
if (len(query_set) == 0):
del request.POST['key_id']
del request.POST['refresh']
return result_empty(request, key_id, "ID not found, please try other...")
file_model = query_set[0]
file_model.date_last_access = file_model.date_last_access_2
file_model.date_last_access_2 = timezone.now()
## try to detect if is finished,
if (file_model.is_finished): ## show the results
pass
elif (file_model.job_sge_id == 0): ### fail submit job
## fail submit job
sz_error = "Fail submit SGE job %s" % (file_model.date_created.strftime("%Y-%m-%d %H:%M"))
return render(request, 'lvb/result.html', {'file_model': file_model, 'error_message': sz_error, 'result': "xpto"} )
else:
submit = clProcessSGE()
n_status_sge_id = submit.get_status_process(file_model.job_sge_id)
if (n_status_sge_id == clProcessSGE.SGE_JOB_ID_FINISH): ## show the results
file_model.date_finished = constants.get_datetime_stop_sge_job(file_model.key_id)
if (file_model.date_finished == None):
sz_error = "Fail to get results from LVb"
return render(request, 'lvb/result.html', {'file_model': file_model, 'error_message': sz_error, 'result': "xpto", 'is_reload_page' : is_reload_page } )
(lvb_starting_temperature, lvb_iterations, lvb_length, lvb_trees, lvb_seed) = submit.get_info_from_lvb_result_file(file_model.key_id)
file_model.lvb_starting_temperature = lvb_starting_temperature
file_model.lvb_iterations = lvb_iterations
file_model.lvb_length = lvb_length
file_model.lvb_trees = lvb_trees
file_model.lvb_seed = lvb_seed
file_model.is_finished = True
request.session[Constants.TAG_SESSION_KEY_ID] = file_model.key_id
elif (n_status_sge_id == clProcessSGE.SGE_JOB_ID_PROCESSING):
file_model.is_processing = True
file_model.is_finished = False
is_reload_page = True
elif (n_status_sge_id == clProcessSGE.SGE_JOB_ID_QUEUE):
file_model.is_processing = True
file_model.is_finished = False
is_reload_page = True
## get information about tree
lvb_message_tree = ""
lvb_tree_output = ""
lvb_output = ""
if (file_model.is_finished):
if (file_model.lvb_trees == 0):
lvb_message_tree = "Zero trees founded..."
elif (file_model.lvb_trees == 1):
lvb_message_tree = "Only one tree obtained..."
lvb_tree_output = constants.get_first_tree(file_model.key_id)
else:
lvb_message_tree = "%d trees obtained but only the first is visible, You can download all of them..."
lvb_tree_output = constants.get_first_tree(file_model.key_id)
lvb_output = constants.get_all_output_lvb(file_model.key_id)
file_model.save()
return render(request, 'lvb/result.html', {'file_model': file_model, 'result': "xpto", 'lvb_message_tree' : lvb_message_tree,
'lvb_tree_output' : lvb_tree_output, 'lvb_output' : lvb_output, 'is_reload_page' : is_reload_page } )