def form_valid(self, form):
# build command strings, create skylabfile for each file input
cluster = form.cleaned_data['mpi_cluster']
input_file = form.cleaned_data['param_input']
exec_string = u"vina_split --input {0:s} ".format(input_file.name)
input_filename_without_ext = os.path.splitext(os.path.basename(input_file.name))[0]
# if form.cleaned_data.get('param_ligand_prefix'):
# exec_string += u"--ligand {0:s} ".format(get_valid_filename(form.cleaned_data['param_ligand_prefix']))
# else:
exec_string += u"--ligand {0:s}-ligand ".format(input_filename_without_ext)
# if form.cleaned_data.get('param_flex_prefix'):
# exec_string += u"--flex {0:s} ".format(get_valid_filename(form.cleaned_data['param_flex_prefix']))
# else:
exec_string += u"--flex {0:s}-flex ".format(input_filename_without_ext)
#print(exec_string)
tool = Tool.objects.get(simple_name="vinasplit")
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user,
task_data=json.dumps({'command_list': [exec_string]})
)
self.kwargs['id'] = task.id # pass to get_success_url
SkyLabFile.objects.create(type=1, file=input_file, task=task)
send_to_queue(task=task)
return super(VinaSplitView, self).form_valid(form)
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
input_file = form.cleaned_data['param_input']
exec_string = u"vina_split --input {0:s} ".format(input_file.name)
input_filename_without_ext = os.path.splitext(os.path.basename(input_file.name))[0]
# if form.cleaned_data.get('param_ligand_prefix'):
# exec_string += u"--ligand {0:s} ".format(get_valid_filename(form.cleaned_data['param_ligand_prefix']))
# else:
exec_string += u"--ligand {0:s}-ligand ".format(input_filename_without_ext)
# if form.cleaned_data.get('param_flex_prefix'):
# exec_string += u"--flex {0:s} ".format(get_valid_filename(form.cleaned_data['param_flex_prefix']))
# else:
exec_string += u"--flex {0:s}-flex ".format(input_filename_without_ext)
#print(exec_string)
tool = Tool.objects.get(simple_name="vinasplit")
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user,
task_data=json.dumps({'command_list': [exec_string]})
)
self.kwargs['id'] = task.id # pass to get_success_url
SkyLabFile.objects.create(type=1, file=input_file, task=task)
send_to_queue(task=task)
return super(VinaSplitView, self).form_valid(form)
def form_valid(self, form):
# build command strings, create skylabfile for file inputs
cluster = form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='dock6')
# -n cluster_size
command = "mpirun -np {0:d} -f {1:s} dock6.mpi ".format(cluster.total_node_count, settings.MPIEXEC_NODES_FILE)
# command = "mpiexec -np 4 dock6.mpi "
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
self.kwargs['id'] = task.id
cluster = form.cleaned_data['mpi_cluster']
input_file = form.cleaned_data['param_input_file']
SkyLabFile.objects.create(type=1, file=input_file, task=task)
command += u"-i {0:s} ".format(input_file.name)
for f in form.cleaned_data['param_other_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
if form.cleaned_data.get('param_output_prefix'):
command += u"-o ../output/{0:s}.out ".format(form.cleaned_data['param_output_prefix'])
else:
command += u"-o ../output/{0:s}.out ".format(os.path.splitext(input_file.name)[0])
task.task_data = json.dumps({'command_list': [command]})
task.save()
send_to_queue(task=task) # send signal to queue this task to task queue
return super(Dock6View, self).form_valid(form)
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='dock6')
# -n cluster_size
command = "mpirun -np {0:d} -f {1:s} dock6.mpi ".format(cluster.total_node_count, settings.MPIEXEC_NODES_FILE)
# command = "mpiexec -np 4 dock6.mpi "
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
self.kwargs['id'] = task.id
cluster = form.cleaned_data['mpi_cluster']
input_file = form.cleaned_data['param_input_file']
SkyLabFile.objects.create(type=1, file=input_file, task=task)
command += u"-i {0:s} ".format(input_file.name)
for f in form.cleaned_data['param_other_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
if form.cleaned_data.get('param_output_prefix'):
command += u"-o ../output/{0:s}.out ".format(form.cleaned_data['param_output_prefix'])
else:
command += u"-o ../output/{0:s}.out ".format(os.path.splitext(input_file.name)[0])
task.task_data = json.dumps({'command_list': [command]})
task.save()
send_to_queue(task=task)
return super(Dock6View, self).form_valid(form)
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='grid')
command = "grid "
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user,
)
self.kwargs['id'] = task.id
input_file = form.cleaned_data['param_input_file']
SkyLabFile.objects.create(type=1, file=input_file, task=task)
command += "-i %s " % input_file.name
for f in form.cleaned_data['param_other_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
if form.cleaned_data.get('param_output_prefix'):
command += "-o ../output/%s.out " % form.cleaned_data['param_output_prefix']
else:
command += "-o ../output/%s.out " % os.path.splitext(input_file.name)[0]
if form.cleaned_data['param_terse']:
command += "-t "
if form.cleaned_data['param_verbose']:
command += "-v "
task.task_data = json.dumps({'command_list': [command]})
task.save()
send_to_queue(task=task)
return super(GridView, self).form_valid(form)
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
receptor_file = form.cleaned_data['param_receptor_file']
exec_string = "autogrid4 "
task = Task.objects.create(
mpi_cluster=cluster, tool=Tool.objects.get(simple_name='autogrid4'), user=self.request.user
)
self.kwargs['id'] = task.id
SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_gpf_file'], task=task)
SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_receptor_file'], task=task)
exec_string += u"-p {0:s} ".format(form.cleaned_data['param_gpf_file'].name)
if form.cleaned_data.get('param_glg_filename'):
exec_string += u"-l ../output/{0:s}.glg ".format(form.cleaned_data['param_glg_filename'])
else:
exec_string += u'-l ../output/{0:s}.glg '.format(
os.path.splitext(form.cleaned_data['param_gpf_file'].name)[0])
if form.cleaned_data['param_d']:
exec_string += "-d "
exec_string += "; "
if form.cleaned_data['param_use_with_autodock']:
SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_ligand_file'], task=task)
SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_dpf_file'], task=task)
exec_string += "autodock4 -p %s " % form.cleaned_data['param_dpf_file'].name
if form.cleaned_data.get('param_dlg_filename'):
exec_string += u"-l ../output/{0:s}.dlg ".format(form.cleaned_data['param_dlg_filename'])
else:
exec_string += u"-l ../output/{0:s}.dlg ".format(
os.path.splitext(form.cleaned_data['param_dpf_file'].name)[0])
if form.cleaned_data['param_k']:
exec_string += "-k "
if form.cleaned_data['param_i']:
exec_string += "-i "
if form.cleaned_data['param_t']:
exec_string += "-t "
if form.cleaned_data['param_d_dock']:
exec_string += "-d "
exec_string += ";"
task.task_data = json.dumps({'command_list': [exec_string]})
task.save()
send_to_queue(task=task)
return super(Autogrid4View, self).form_valid(form)
def post(self, request, *args, **kwargs):
# build command, strings, create SkylabFile instances for each input file
form_class = self.get_form_class()
select_mpi_form = self.get_form(form_class)
input_formset = self.input_formset(request.POST, request.FILES)
if select_mpi_form.is_valid() and input_formset.is_valid():
cluster = select_mpi_form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='impi')
command_list = []
for input_form in input_formset:
operation = input_form.cleaned_data.get('param_operation')
# command = {}
if operation:
# command['operation'] = operation
command_list.append(operation)
if operation == '3' or operation == '4':
value = input_form.cleaned_data.get('param_value')
command_list.append(value)
# command['value'] = value
# command_list.append(command)
task = Task.objects.create(mpi_cluster=cluster,
tool=tool,
user=self.request.user)
input_filenames = []
for f in select_mpi_form.cleaned_data['input_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
input_filenames.append(f.name)
task_data = {
'command_list': command_list,
'input_filenames': input_filenames
}
task.refresh_from_db()
task.task_data = json.dumps(task_data)
task.save() # send signal to queue this task to task queue
send_to_queue(task=task)
return redirect('task_detail_view', pk=task.id)
else:
return render(
request, 'modules/impi/use_impi.html', {
'form': select_mpi_form,
'input_formset': input_formset,
'tool': Tool.objects.get(simple_name='impi'),
})
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
# BUILD COMMAND STRING, CREATE SKYLABFILE INSTANCES FOR FILE INPUTS
exec_string = "autodock4 "
task = Task.objects.create(
mpi_cluster=cluster,
tool=Tool.objects.get(simple_name='autodock4'),
user=self.request.user)
self.kwargs['id'] = task.id
# SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_receptor_file'], task=task)
SkyLabFile.objects.create(type=1,
file=form.cleaned_data['param_ligand_file'],
task=task)
SkyLabFile.objects.create(type=1,
file=form.cleaned_data['param_dpf_file'],
task=task)
exec_string += "-p %s " % form.cleaned_data['param_dpf_file'].name
for grid_file in form.cleaned_data['param_grid_files']:
SkyLabFile.objects.create(type=1, file=grid_file, task=task)
if form.cleaned_data.get('param_dlg_filename'):
exec_string += "-l ../output/%s.dlg " % (
form.cleaned_data['param_dlg_filename'])
else:
exec_string += "-l ../output/%s.dlg " % os.path.splitext(
form.cleaned_data['param_dpf_file'].name)[0]
if form.cleaned_data['param_k']:
exec_string += "-k "
if form.cleaned_data['param_i']:
exec_string += "-i "
if form.cleaned_data['param_t']:
exec_string += "-t "
if form.cleaned_data['param_d']:
exec_string += "-d "
exec_string += ";"
task.task_data = json.dumps({'command_list': [exec_string]})
task.save()
send_to_queue(task=task) # send signal to queue this task
return super(Autodock4View, self).form_valid(form)
def post(self, request, *args, **kwargs):
form_class = self.get_form_class()
select_mpi_form = self.get_form(form_class)
input_formset = self.input_formset(request.POST, request.FILES)
if select_mpi_form.is_valid() and input_formset.is_valid():
cluster = select_mpi_form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='impi')
command_list = []
for input_form in input_formset:
operation = input_form.cleaned_data.get('param_operation')
# command = {}
if operation:
# command['operation'] = operation
command_list.append(operation)
if operation == '3' or operation == '4':
value = input_form.cleaned_data.get('param_value')
command_list.append(value)
# command['value'] = value
# command_list.append(command)
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
input_filenames = []
for f in select_mpi_form.cleaned_data['input_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
input_filenames.append(f.name)
task_data = {
'command_list': command_list,
'input_filenames': input_filenames
}
task.refresh_from_db()
task.task_data = json.dumps(task_data)
task.save()
send_to_queue(task=task)
return redirect('task_detail_view', pk=task.id)
else:
return render(request, 'modules/impi/use_impi.html', {
'form': select_mpi_form,
'input_formset': input_formset,
'tool':Tool.objects.get(simple_name='impi'),
})
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
exec_string = "autodock4 "
task = Task.objects.create(
mpi_cluster=cluster, tool=Tool.objects.get(simple_name='autodock4'), user=self.request.user
)
self.kwargs['id'] = task.id
# SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_receptor_file'], task=task)
SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_ligand_file'], task=task)
SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_dpf_file'], task=task)
exec_string += "-p %s " % form.cleaned_data['param_dpf_file'].name
for grid_file in form.cleaned_data['param_grid_files']:
SkyLabFile.objects.create(type=1, file=grid_file, task=task)
# if form.cleaned_data.get('param_dat_file'):
# SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_dat_file'], task=task)
if form.cleaned_data.get('param_dlg_filename'):
exec_string += "-l ../output/%s.dlg " % (form.cleaned_data['param_dlg_filename'])
else:
exec_string += "-l ../output/%s.dlg " % os.path.splitext(form.cleaned_data['param_dpf_file'].name)[0]
if form.cleaned_data['param_k']:
exec_string += "-k "
if form.cleaned_data['param_i']:
exec_string += "-i "
if form.cleaned_data['param_t']:
exec_string += "-t "
if form.cleaned_data['param_d']:
exec_string += "-d "
exec_string += ";"
task.task_data = json.dumps({'command_list': [exec_string]})
task.save()
send_to_queue(task=task)
# find a way to know if thread is already running
return super(Autodock4View, self).form_valid(form)
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='gamess')
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
command_list = []
for f in form.cleaned_data['input_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
filename_without_ext = os.path.splitext(f.name)[0]
command = "rungms {0} 01 1 2>&1 | tee ../output/{0}.log".format(filename_without_ext)
command_list.append(command)
task.refresh_from_db()
task.task_data = json.dumps({'command_list': command_list})
task.save()
send_to_queue(task=task)
self.kwargs['id'] = task.id
return super(GamessView, self).form_valid(form)
def form_valid(self, form):
# build command strings, create SkylabFiles for form input files
cluster = form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='gamess')
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
command_list = []
for f in form.cleaned_data['input_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
filename_without_ext = os.path.splitext(f.name)[0]
command = "rungms {0} 01 1 2>&1 | tee ../output/{0}.log".format(filename_without_ext)
command_list.append(command)
task.refresh_from_db()
task.task_data = json.dumps({'command_list': command_list})
task.save()
send_to_queue(task=task) # send signal to queue this task to task queue
self.kwargs['id'] = task.id
return super(GamessView, self).form_valid(form)
def form_valid(self, form):
# build command strings, create skylabfile for file inputs
cluster = form.cleaned_data['mpi_cluster']
tool = Tool.objects.get(simple_name='grid')
command = "grid "
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user,
)
self.kwargs['id'] = task.id
input_file = form.cleaned_data['param_input_file']
SkyLabFile.objects.create(type=1, file=input_file, task=task)
command += "-i %s " % input_file.name
for f in form.cleaned_data['param_other_files']:
SkyLabFile.objects.create(type=1, file=f, task=task)
if form.cleaned_data.get('param_output_prefix'):
command += "-o ../output/%s.out " % form.cleaned_data['param_output_prefix']
else:
command += "-o ../output/%s.out " % os.path.splitext(input_file.name)[0]
if form.cleaned_data['param_terse']:
command += "-t "
if form.cleaned_data['param_verbose']:
command += "-v "
task.task_data = json.dumps({'command_list': [command]})
task.save()
send_to_queue(task=task) # send signal to queue this task to task queue
return super(GridView, self).form_valid(form)
def post(self, request, *args, **kwargs):
form_class = self.get_form_class()
select_mpi_form = self.get_form(form_class)
input_formset = self.input_formset(request.POST, request.FILES)
other_parameter_form = OtherParameterForm(request.POST, request.FILES)
if select_mpi_form.is_valid() and other_parameter_form.is_valid(
) and input_formset.is_valid():
# build command strings, create skylab file for each file input
cluster = select_mpi_form.cleaned_data['mpi_cluster']
command_list = []
# -n cluster_size
command = "mpiexec -n {0:d} -f {1:s} ".format(
cluster.total_node_count, settings.MPIEXEC_NODES_FILE)
# -bynode
if select_mpi_form.cleaned_data['param_bynode']:
command += "-bynode "
tool = Tool.objects.get(simple_name="ray")
task = Task.objects.create(mpi_cluster=cluster,
tool=tool,
user=self.request.user)
command += "Ray -o task_{0:d}/output ".format(task.id)
# k-mer length
if other_parameter_form.cleaned_data.get('param_kmer_length'):
command += u"-k {0:d}".format(
other_parameter_form.cleaned_data["param_kmer_length"])
# -mini-ranks-per-rank
if select_mpi_form.cleaned_data.get('param_mini_ranks'):
command += u"-mini-ranks-per-rank {0:d} ".format(
select_mpi_form.cleaned_data["param_mini_ranks"])
for form in input_formset:
parameter = form.cleaned_data.get('parameter')
if parameter: # ignore blank parameter value
input_file1 = form.cleaned_data['input_file1']
instance = SkyLabFile.objects.create(type=1,
file=input_file1,
task=task)
# filepath1 = create_input_skylab_file(task, 'input', input_file1)
filepath1 = instance.file.name
if parameter == "-p":
input_file2 = form.cleaned_data['input_file2']
instance = SkyLabFile.objects.create(type=1,
file=input_file2,
task=task)
# filepath2 = create_input_skylab_file(task, 'input', input_file2)
filepath2 = instance.file.name
command += "{0:s} {1:s} {2:s} ".format(
parameter, filepath1, filepath2)
elif parameter == "-s" or parameter == "-i":
command += "{0:s} {1:s} ".format(parameter, filepath1)
if other_parameter_form.cleaned_data['param_run_surveyor']:
command += "-run-surveyor "
if other_parameter_form.cleaned_data['param_read_sample_graph']:
for index, f in other_parameter_form.cleaned_data[
'subparam_graph_files']:
instance = SkyLabFile.objects.create(
type=1, upload_path='input/graph', file=f, task=task)
filepath = instance.file.name
# filepath = create_input_skylab_file(task, 'input/graph', f)
command += "-read-sample-graph graph-{0:d} {1:s} ".format(
index, filepath)
if other_parameter_form.cleaned_data['param_search']:
command += "-search task_{0:d}/input/search ".format(task.id)
for f in other_parameter_form.cleaned_data[
'subparam_search_files']:
SkyLabFile.objects.create(type=1,
upload_path='input/search',
file=f,
task=task)
if other_parameter_form.cleaned_data['param_one_color_per_file']:
command += "-one-color-per-file "
if other_parameter_form.cleaned_data['param_with_taxonomy']:
genome_to_taxon_file = other_parameter_form.cleaned_data[
'subparam_genome_to_taxon_file']
tree_of_life_edges_file = other_parameter_form.cleaned_data[
'subparam_tree_of_life_edges_file']
taxon_names_file = other_parameter_form.cleaned_data[
'subparam_taxon_names_file']
instance = SkyLabFile.objects.create(
type=1,
upload_path='input/taxonomy',
file=genome_to_taxon_file,
task=task)
genome_filepath = instance.file.name
instance = SkyLabFile.objects.create(
type=1,
upload_path='input/taxonomy',
file=tree_of_life_edges_file,
task=task)
tree_filepath = instance.file.name
instance = SkyLabFile.objects.create(
type=1,
upload_path='input/taxonomy',
file=taxon_names_file,
task=task)
taxon_filepath = instance.file.name
command += "-with-taxonomy {0:s} {1:s} {2:s} ".format(
genome_filepath, tree_filepath, taxon_filepath)
if other_parameter_form.cleaned_data['param_gene_ontology']:
annotations_file = other_parameter_form.cleaned_data[
'subparam_annotations_file']
SkyLabFile.objects.create(type=1,
upload_path='input/gene_ontology',
file=annotations_file,
task=task)
command += "-gene-ontology task_{0:d}/input/OntologyTerms.txt {1:s} ".format(
task.id, annotations_file.name)
command_list.append(
"wget -q -O task_{0:d}/input/OntologyTerms.txt http://geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo"
.format(task.id))
# Other Output options
if other_parameter_form.cleaned_data[
'param_enable_neighbourhoods']:
command += "-enable-neighbourhoods "
if other_parameter_form.cleaned_data['param_amos']:
command += "-amos "
if other_parameter_form.cleaned_data['param_write_kmers']:
command += "-write-kmers "
if other_parameter_form.cleaned_data['param_graph_only']:
command += "-graph-only "
if other_parameter_form.cleaned_data['param_write_read_markers']:
command += "-write-read-markers "
if other_parameter_form.cleaned_data['param_write_seeds']:
command += "-write-seeds "
if other_parameter_form.cleaned_data['param_write_extensions']:
command += "-write-extensions "
if other_parameter_form.cleaned_data['param_write_contig_paths']:
command += "-write-contig-paths "
if other_parameter_form.cleaned_data['param_write_marker_summary']:
command += "-write-marker-summary "
# Memory usage
if other_parameter_form.cleaned_data['param_show_memory_usage']:
command += "-show-memory-usage "
if other_parameter_form.cleaned_data[
'param_show_memory_allocations']:
command += "-show-memory-allocations "
# Algorithm verbosity
if other_parameter_form.cleaned_data[
'param_show_extension_choice']:
command += "-show-extension-choice "
if other_parameter_form.cleaned_data['param_show_ending_context']:
command += "-show-ending-context "
if other_parameter_form.cleaned_data[
"param_show_distance_summary"]:
command += "-show-distance-summary "
if other_parameter_form.cleaned_data['param_show_consensus']:
command += "-show-consensus "
command_list.append(command)
task.task_data = json.dumps({'command_list': command_list})
task.save()
send_to_queue(
task=task) # send signal to queue this task to task queue
return redirect('task_detail_view', pk=task.id)
# return redirect(reverse('task_detailview', kwargs={'pk': task.id}))
else:
return render(
request, 'modules/ray/use_ray.html', {
'form': select_mpi_form,
'other_parameter_form': other_parameter_form,
'input_formset': input_formset,
'tool': Tool.objects.get(simple_name="ray")
})
def form_valid(self, form):
# build command strings, create skylabfile for each file input
cluster = form.cleaned_data['mpi_cluster']
# exec_string_template = "mkdir -p {outpath}; vina " #todo: test if runs properly
exec_string_template = "vina "
tool = Tool.objects.get(simple_name="vina")
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
instance = SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_receptor'], task=task)
receptor_filepath = instance.file.name
exec_string_template += u"--receptor {0:s} ".format(receptor_filepath)
if form.cleaned_data.get('param_flex'):
instance = SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_flex'], task=task)
flex_filepath = instance.file.name
exec_string_template += "--flex %s " % flex_filepath
exec_string_template += "--ligand {filepath} --out {outpath}/vina_out.pdbqt --log {outpath}/log.txt "
# if form.cleaned_data['param_score_only']: # search space not required
# exec_string_template += "--score_only "
# else: # search space required
center_x = form.cleaned_data['param_center_x']
center_y = form.cleaned_data['param_center_y']
center_z = form.cleaned_data['param_center_z']
size_x = form.cleaned_data['param_size_x']
size_y = form.cleaned_data['param_size_y']
size_z = form.cleaned_data['param_size_z']
exec_string_template += "--center_x {0} --center_y {1} --center_z {2} --size_x {3} --size_y {4} --size_z {5} ".format(
center_x, center_y, center_z, size_x, size_y, size_z)
if form.cleaned_data.get('param_seed'):
exec_string_template += "--seed {0} ".format(form.cleaned_data['param_seed'])
if form.cleaned_data.get('param_exhaustiveness'):
exec_string_template += "--exhaustiveness {0} ".format(form.cleaned_data['param_exhaustiveness'])
if form.cleaned_data.get('param_num_modes'):
exec_string_template += "--num_modes {0} ".format(form.cleaned_data['param_num_modes'])
if form.cleaned_data.get('param_energy_range'):
exec_string_template += "--energy_range {0} ".format(form.cleaned_data['param_energy_range'])
# if form.cleaned_data['param_local_only']:
# exec_string_template += "--local_only "
#
# if form.cleaned_data['param_randomize_only']:
# exec_string_template += "--randomize_only "
#
# if form.cleaned_data.get('param_weight_gauss1'):
# exec_string_template += "--weight_gauss1 {0:s} ".format(form.cleaned_data['param_weight_gauss1'])
#
# if form.cleaned_data.get('param_weight_gauss2'):
# exec_string_template += "--weight_gauss2 {0:s} ".format(form.cleaned_data['param_weight_gauss2'])
#
# if form.cleaned_data.get('param_weight_repulsion'):
# exec_string_template += "--weight_repulsion {0:s} ".format(
# form.cleaned_data['param_weight_repulsion'])
#
# if form.cleaned_data.get('param_weight_hydrophobic'):
# exec_string_template += "--weight_hydrophobic {0:s} ".format(
# form.cleaned_data['param_weight_hydrophobic'])
#
# if form.cleaned_data.get('param_weight_hydrogen'):
# exec_string_template += "--weight_hydrogen {0:s} ".format(
# form.cleaned_data['param_weight_hydrogen'])
#
# if form.cleaned_data.get('param_weight_rot'):
# exec_string_template += "--weight_rot {0:s} ".format(form.cleaned_data['param_weight_rot'])
exec_string_template += "; "
# build commands
command_list = []
task_remote_subdirs = ['input', 'output']
for f in form.cleaned_data['param_ligands']:
instance = SkyLabFile.objects.create(type=1, upload_path='input/ligands', file=f, task=task)
filepath = instance.file.name
# filepath = create_input_skylab_file(task, 'input/ligands', f)
filename_without_ext = os.path.splitext(f.name)[0]
task_remote_subdir = 'output/' + filename_without_ext
outpath = os.path.join(task.task_dirname, task_remote_subdir)
task_remote_subdirs.append(task_remote_subdir)
command_list.append(exec_string_template.format(outpath=outpath, filepath=filepath))
task.task_data = json.dumps({'command_list': command_list, 'task_remote_subdirs': task_remote_subdirs})
task.save()
send_to_queue(task=task)
self.kwargs['task_id'] = task.id
return super(VinaView, self).form_valid(form)
def post(self, request, *args, **kwargs):
form_class = self.get_form_class()
select_mpi_form = self.get_form(form_class)
input_formset = self.input_formset(request.POST, request.FILES)
if select_mpi_form.is_valid() and input_formset.is_valid():
# build command strings, create skylabfile for each file input
cluster = select_mpi_form.cleaned_data['mpi_cluster']
# based on intial environment variables config on quantum espresso
para_prefix = "mpirun -np {0:d} -f {1:s} ".format(
cluster.total_node_count, settings.MPIEXEC_NODES_FILE)
para_postfix = "-nk 1 -nd 1 -nb 1 -nt 1 "
# copied from espresso's default env var value
para_image_prefix = "mpirun -np 4"
param_image_postfix = '-ni 2 {0}'.format(para_postfix)
tool = Tool.objects.get(simple_name='quantumespresso')
task = Task.objects.create(mpi_cluster=cluster,
tool=tool,
user=self.request.user)
# build command list
command_list = []
jsmol_output_files = []
# in form clean pseudopotentials field returns json dict
task_data = json.loads(
select_mpi_form.cleaned_data['param_pseudopotentials'])
#location of quantum espresso executables
remote_bin_dir = "/mirror/espresso-5.4.0/bin"
for form in input_formset:
executable = form.cleaned_data.get('param_executable', None)
input_file = form.cleaned_data.get("param_input_file", None)
if executable and input_file: # ignore blank parameter value
instance = SkyLabFile.objects.create(type=1,
file=input_file,
task=task)
# neb.x -inp filename.in
# ph.x can be run using images #not supported
output_filename = '{0}.out'.format(
os.path.splitext(input_file.name)[0])
if executable == "neb.x":
command_list.append(
'{0} {1} {2} -inp input/{3} > output/{4}'.format(
para_prefix,
os.path.join(remote_bin_dir,
executable), para_postfix,
input_file.name, output_filename))
else: # at least for pw.x, cp.x
command_list.append(
'{0} {1} {2} < input/{3} > output/{4}'.format(
para_prefix,
os.path.join(remote_bin_dir,
executable), para_postfix,
input_file.name, output_filename))
if executable == "pw.x": #identify expected output as compatible for jsmol
jsmol_output_files.append(output_filename)
task_data['command_list'] = command_list
task_data['jsmol_output_files'] = jsmol_output_files
task.task_data = json.dumps(task_data)
task.save()
send_to_queue(task=task) # send signal to queue task to task queue
return redirect('task_detail_view', pk=task.id)
else:
return render(
request, 'modules/quantum espresso/use_quantum_espresso.html',
{
'form': select_mpi_form,
'input_formset': input_formset,
'tool': Tool.objects.get(simple_name='quantumespresso'),
})
def post(self, request, *args, **kwargs):
form_class = self.get_form_class()
select_mpi_form = self.get_form(form_class)
input_formset = self.input_formset(request.POST, request.FILES)
other_parameter_form = OtherParameterForm(request.POST, request.FILES)
if select_mpi_form.is_valid() and other_parameter_form.is_valid() and input_formset.is_valid():
cluster = select_mpi_form.cleaned_data['mpi_cluster']
command_list = []
# -n cluster_size
command = "mpiexec -n {0:d} -f {1:s} ".format(cluster.total_node_count, settings.MPIEXEC_NODES_FILE)
# -bynode
if select_mpi_form.cleaned_data['param_bynode']:
command += "-bynode "
tool = Tool.objects.get(simple_name="ray")
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
command += "Ray -o task_{0:d}/output ".format(task.id)
# k-mer length
if other_parameter_form.cleaned_data.get('param_kmer_length'):
command += u"-k {0:d}".format(other_parameter_form.cleaned_data["param_kmer_length"])
# -mini-ranks-per-rank
if select_mpi_form.cleaned_data.get('param_mini_ranks'):
command += u"-mini-ranks-per-rank {0:d} ".format(select_mpi_form.cleaned_data["param_mini_ranks"])
for form in input_formset:
parameter = form.cleaned_data.get('parameter')
if parameter: # ignore blank parameter value
input_file1 = form.cleaned_data['input_file1']
instance = SkyLabFile.objects.create(type=1, file=input_file1, task=task)
# filepath1 = create_input_skylab_file(task, 'input', input_file1)
filepath1 = instance.file.name
if parameter == "-p":
input_file2 = form.cleaned_data['input_file2']
instance = SkyLabFile.objects.create(type=1, file=input_file2, task=task)
# filepath2 = create_input_skylab_file(task, 'input', input_file2)
filepath2 = instance.file.name
command += "{0:s} {1:s} {2:s} ".format(parameter, filepath1, filepath2)
elif parameter == "-s" or parameter == "-i":
command += "{0:s} {1:s} ".format(parameter, filepath1)
if other_parameter_form.cleaned_data['param_run_surveyor']:
command += "-run-surveyor "
if other_parameter_form.cleaned_data['param_read_sample_graph']:
for index, f in other_parameter_form.cleaned_data['subparam_graph_files']:
instance = SkyLabFile.objects.create(type=1, upload_path='input/graph', file=f, task=task)
filepath = instance.file.name
# filepath = create_input_skylab_file(task, 'input/graph', f)
command += "-read-sample-graph graph-{0:d} {1:s} ".format(index, filepath)
if other_parameter_form.cleaned_data['param_search']:
command += "-search task_{0:d}/input/search ".format(task.id)
for f in other_parameter_form.cleaned_data['subparam_search_files']:
SkyLabFile.objects.create(type=1, upload_path='input/search', file=f, task=task)
if other_parameter_form.cleaned_data['param_one_color_per_file']:
command += "-one-color-per-file "
if other_parameter_form.cleaned_data['param_with_taxonomy']:
genome_to_taxon_file = other_parameter_form.cleaned_data['subparam_genome_to_taxon_file']
tree_of_life_edges_file = other_parameter_form.cleaned_data['subparam_tree_of_life_edges_file']
taxon_names_file = other_parameter_form.cleaned_data['subparam_taxon_names_file']
instance = SkyLabFile.objects.create(type=1, upload_path='input/taxonomy', file=genome_to_taxon_file,
task=task)
genome_filepath = instance.file.name
instance = SkyLabFile.objects.create(type=1, upload_path='input/taxonomy', file=tree_of_life_edges_file,
task=task)
tree_filepath = instance.file.name
instance = SkyLabFile.objects.create(type=1, upload_path='input/taxonomy', file=taxon_names_file,
task=task)
taxon_filepath = instance.file.name
command += "-with-taxonomy {0:s} {1:s} {2:s} ".format(genome_filepath, tree_filepath, taxon_filepath)
if other_parameter_form.cleaned_data['param_gene_ontology']:
annotations_file = other_parameter_form.cleaned_data['subparam_annotations_file']
SkyLabFile.objects.create(type=1, upload_path='input/gene_ontology', file=annotations_file, task=task)
command += "-gene-ontology task_{0:d}/input/OntologyTerms.txt {1:s} ".format(task.id,
annotations_file.name)
command_list.append(
"wget -q -O task_{0:d}/input/OntologyTerms.txt http://geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo".format(
task.id))
# Other Output options
if other_parameter_form.cleaned_data['param_enable_neighbourhoods']:
command += "-enable-neighbourhoods "
if other_parameter_form.cleaned_data['param_amos']:
command += "-amos "
if other_parameter_form.cleaned_data['param_write_kmers']:
command += "-write-kmers "
if other_parameter_form.cleaned_data['param_graph_only']:
command += "-graph-only "
if other_parameter_form.cleaned_data['param_write_read_markers']:
command += "-write-read-markers "
if other_parameter_form.cleaned_data['param_write_seeds']:
command += "-write-seeds "
if other_parameter_form.cleaned_data['param_write_extensions']:
command += "-write-extensions "
if other_parameter_form.cleaned_data['param_write_contig_paths']:
command += "-write-contig-paths "
if other_parameter_form.cleaned_data['param_write_marker_summary']:
command += "-write-marker-summary "
# Memory usage
if other_parameter_form.cleaned_data['param_show_memory_usage']:
command += "-show-memory-usage "
if other_parameter_form.cleaned_data['param_show_memory_allocations']:
command += "-show-memory-allocations "
# Algorithm verbosity
if other_parameter_form.cleaned_data['param_show_extension_choice']:
command += "-show-extension-choice "
if other_parameter_form.cleaned_data['param_show_ending_context']:
command += "-show-ending-context "
if other_parameter_form.cleaned_data["param_show_distance_summary"]:
command += "-show-distance-summary "
if other_parameter_form.cleaned_data['param_show_consensus']:
command += "-show-consensus "
command_list.append(command)
task.task_data = json.dumps({'command_list': command_list})
task.save()
send_to_queue(task=task)
return redirect('task_detail_view', pk=task.id)
# return redirect(reverse('task_detailview', kwargs={'pk': task.id}))
else:
return render(request, 'modules/ray/use_ray.html', {
'form': select_mpi_form,
'other_parameter_form': other_parameter_form,
'input_formset': input_formset,
'tool':Tool.objects.get(simple_name="ray")
})
def form_valid(self, form):
cluster = form.cleaned_data['mpi_cluster']
# exec_string_template = "mkdir -p {outpath}; vina " #todo: test if runs properly
exec_string_template = "vina "
tool = Tool.objects.get(simple_name="vina")
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
instance = SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_receptor'], task=task)
receptor_filepath = instance.file.name
exec_string_template += u"--receptor {0:s} ".format(receptor_filepath)
if form.cleaned_data.get('param_flex'):
instance = SkyLabFile.objects.create(type=1, file=form.cleaned_data['param_flex'], task=task)
flex_filepath = instance.file.name
exec_string_template += "--flex %s " % flex_filepath
exec_string_template += "--ligand {filepath} --out {outpath}/vina_out.pdbqt --log {outpath}/log.txt "
# if form.cleaned_data['param_score_only']: # search space not required
# exec_string_template += "--score_only "
# else: # search space required
center_x = form.cleaned_data['param_center_x']
center_y = form.cleaned_data['param_center_y']
center_z = form.cleaned_data['param_center_z']
size_x = form.cleaned_data['param_size_x']
size_y = form.cleaned_data['param_size_y']
size_z = form.cleaned_data['param_size_z']
exec_string_template += "--center_x {0} --center_y {1} --center_z {2} --size_x {3} --size_y {4} --size_z {5} ".format(
center_x, center_y, center_z, size_x, size_y, size_z)
if form.cleaned_data.get('param_seed'):
exec_string_template += "--seed {0} ".format(form.cleaned_data['param_seed'])
if form.cleaned_data.get('param_exhaustiveness'):
exec_string_template += "--exhaustiveness {0} ".format(form.cleaned_data['param_exhaustiveness'])
if form.cleaned_data.get('param_num_modes'):
exec_string_template += "--num_modes {0} ".format(form.cleaned_data['param_num_modes'])
if form.cleaned_data.get('param_energy_range'):
exec_string_template += "--energy_range {0} ".format(form.cleaned_data['param_energy_range'])
# if form.cleaned_data['param_local_only']:
# exec_string_template += "--local_only "
#
# if form.cleaned_data['param_randomize_only']:
# exec_string_template += "--randomize_only "
#
# if form.cleaned_data.get('param_weight_gauss1'):
# exec_string_template += "--weight_gauss1 {0:s} ".format(form.cleaned_data['param_weight_gauss1'])
#
# if form.cleaned_data.get('param_weight_gauss2'):
# exec_string_template += "--weight_gauss2 {0:s} ".format(form.cleaned_data['param_weight_gauss2'])
#
# if form.cleaned_data.get('param_weight_repulsion'):
# exec_string_template += "--weight_repulsion {0:s} ".format(
# form.cleaned_data['param_weight_repulsion'])
#
# if form.cleaned_data.get('param_weight_hydrophobic'):
# exec_string_template += "--weight_hydrophobic {0:s} ".format(
# form.cleaned_data['param_weight_hydrophobic'])
#
# if form.cleaned_data.get('param_weight_hydrogen'):
# exec_string_template += "--weight_hydrogen {0:s} ".format(
# form.cleaned_data['param_weight_hydrogen'])
#
# if form.cleaned_data.get('param_weight_rot'):
# exec_string_template += "--weight_rot {0:s} ".format(form.cleaned_data['param_weight_rot'])
exec_string_template += "; "
# build commands
command_list = []
task_remote_subdirs = ['input', 'output']
for f in form.cleaned_data['param_ligands']:
instance = SkyLabFile.objects.create(type=1, upload_path='input/ligands', file=f, task=task)
filepath = instance.file.name
# filepath = create_input_skylab_file(task, 'input/ligands', f)
filename_without_ext = os.path.splitext(f.name)[0]
task_remote_subdir = 'output/' + filename_without_ext
outpath = os.path.join(task.task_dirname, task_remote_subdir)
task_remote_subdirs.append(task_remote_subdir)
command_list.append(exec_string_template.format(outpath=outpath, filepath=filepath))
task.task_data = json.dumps({'command_list': command_list, 'task_remote_subdirs': task_remote_subdirs})
task.save()
send_to_queue(task=task)
self.kwargs['task_id'] = task.id
return super(VinaView, self).form_valid(form)
def post(self, request, *args, **kwargs):
form_class = self.get_form_class()
select_mpi_form = self.get_form(form_class)
input_formset = self.input_formset(request.POST, request.FILES)
if select_mpi_form.is_valid() and input_formset.is_valid():
# do something with the cleaned_data on the formsets.
# print select_mpi_form.cleaned_data.get('mpi_cluster')
cluster = select_mpi_form.cleaned_data['mpi_cluster']
# based on intial environment variables config on quantum espresso
para_prefix = "mpirun -np {0:d} -f {1:s} ".format(cluster.total_node_count, settings.MPIEXEC_NODES_FILE)
para_postfix = "-nk 1 -nd 1 -nb 1 -nt 1 "
# copied from espresso's default env var value
para_image_prefix = "mpirun -np 4"
param_image_postfix = '-ni 2 {0}'.format(para_postfix)
tool = Tool.objects.get(simple_name='quantumespresso')
task = Task.objects.create(
mpi_cluster=cluster, tool=tool, user=self.request.user
)
# build command list
command_list = []
jsmol_output_files = []
# in form clean pseudopotentials field returns json dict
task_data = json.loads(select_mpi_form.cleaned_data['param_pseudopotentials'])
#location of quantum espresso executables
remote_bin_dir = "/mirror/espresso-5.4.0/bin"
for form in input_formset:
executable = form.cleaned_data.get('param_executable', None)
input_file = form.cleaned_data.get("param_input_file", None)
if executable and input_file: # ignore blank parameter value
instance = SkyLabFile.objects.create(type=1, file=input_file, task=task)
# neb.x -inp filename.in
# ph.x can be run using images #not supported
output_filename = '{0}.out'.format(os.path.splitext(input_file.name)[0])
if executable == "neb.x":
command_list.append(
'{0} {1} {2} -inp input/{3} > output/{4}'.format(para_prefix, os.path.join(remote_bin_dir,executable),
para_postfix,
input_file.name,
output_filename)
)
else: # at least for pw.x, cp.x
command_list.append('{0} {1} {2} < input/{3} > output/{4}'.format(
para_prefix, os.path.join(remote_bin_dir,executable), para_postfix, input_file.name,
output_filename)
)
if executable == "pw.x": #identify expected output as compatible for jsmol
jsmol_output_files.append(output_filename)
task_data['command_list'] = command_list
task_data['jsmol_output_files'] = jsmol_output_files
task.task_data = json.dumps(task_data)
task.save()
send_to_queue(task=task)
return redirect('task_detail_view', pk=task.id)
else:
return render(request, 'modules/quantum espresso/use_quantum_espresso.html', {
'form': select_mpi_form,
'input_formset': input_formset,
'tool': Tool.objects.get(simple_name='quantumespresso'),
})
