def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, ontology_id, filename, file_type, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
log = MessageLog()
log.title = "Biological feature annotation"
log.message = "Status: error, Task: " + task_id + ", User: "******", Error: " + str(exc)
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
message = Message(type='error', title='Error', message=str(exc))
message.send_to(channel)
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, experiment_id, keep_platform, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
exp = Experiment.objects.using(compendium.compendium_nick_name).get(id=experiment_id)
parsing_db = init_parsing(compendium_id, experiment_id)
log = MessageLog()
log.title = "Experiment: " + exp.experiment_access_id + " imported"
log.message = "Status: error, Experiment: " + exp.experiment_access_id + ", Task: " + task_id + ", User: "******", Exception: " \
+ str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
# delete CSV file
for fl in glob.glob(parsing_db + '*.csv'):
os.remove(fl)
message = Message(type='error', title='Error on importing experiment ' + exp.experiment_access_id, message=str(exc))
message.send_to(channel)
data_ready_status = Status.objects.using(compendium.compendium_nick_name).get(name='experiment_data_ready')
exp.status = data_ready_status
exp.save(using=compendium.compendium_nick_name)
Group("compendium_" + str(compendium_id) + "_" + str(experiment_id)).send({
'text': json.dumps({
'stream': view,
'payload': {
'request': {'operation': 'refresh'},
'data': None
}
})
})
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, term, db_id, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
log = MessageLog()
log.title = "Search experiment " + term
log.message = "Status: error, Term: " + term + ", Task: " + task_id + ", User: "******"Exception: " + str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
message = Message(type='error', title='Error', message=str(exc))
message.send_to(channel)
ViewTask.objects.using(compendium.compendium_nick_name). \
get(task_id=task_id, operation=operation, view=view).delete()
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, plt_dir, platform_id, filter_id, \
blast_file_name, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
log = MessageLog()
plt = Platform.objects.using(
compendium.compendium_nick_name).get(id=platform_id)
log.title = "Platform: " + plt.platform_access_id + " importing mapping error"
log.message = "Status: error, Platform: " + plt.platform_access_id + \
", Task: " + task_id + ", User: "******", Exception: " + str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
message = Message(type='error',
title='Error during importing platform mapping',
message=str(exc))
message.send_to(channel)
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, experiment_id, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
exp = Experiment.objects.using(compendium.compendium_nick_name).get(id=experiment_id)
parsing_db = init_parsing(compendium_id, experiment_id)
platforms = [plt.platform_access_id for plt in ParsingPlatform.objects.using(parsing_db).all()]
log = MessageLog()
log.title = "Platforms: " + ", ".join(platforms) + " error"
log.message = "Status: error, Platforms: " + ", ".join(platforms) + ", Experiment: " + \
exp.experiment_access_id + ", Task: " + task_id + ", User: "******", Exception: " \
+ str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
# delete CSV file
for fl in glob.glob(parsing_db + '*bio_feature*.csv'):
os.remove(fl)
message = Message(type='error', title='Error on importing platforms for experiment ' + exp.experiment_access_id, message=str(exc))
message.send_to(channel)
for parsing_platform in ParsingPlatform.objects.using(parsing_db).all():
plt = Platform.objects.using(compendium.compendium_nick_name).get(id=parsing_platform.platform_fk)
plt.status = None
plt.save(using=compendium.compendium_nick_name)
Group("compendium_" + str(compendium_id) + "_" + str(experiment_id)).send({
'text': json.dumps({
'stream': view,
'payload': {
'request': {'operation': 'refresh'},
'data': None
}
})
})
def on_success(self, retval, task_id, args, kwargs):
user_id, compendium_id, ontology_id, filename, file_type, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
log = MessageLog()
log.title = "Biological feature annotation"
log.message = "Status: success, Task: " + task_id + ", User: "******"compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
def delete_bio_feature_annotation(request, *args, **kwargs):
req = request.POST
comp_id = req['compendium_id']
view = req['view']
channel_name = request.session['channel_name']
operation = req['operation']
compendium = CompendiumDatabase.objects.get(id=comp_id)
BioFeatureAnnotation.objects.using(
compendium.compendium_nick_name).all().delete()
message = Message(
type='info',
title='Annotation',
message='Biological feature annotation has been deleted')
message.send_to(Channel(channel_name))
Group("compendium_" + str(comp_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
return HttpResponse(json.dumps({'success': True}),
content_type="application/json")
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, exp_id, exp_name, exp_descr, exp_structure_file, exp_data_file, \
channel_name, view, operation = args
channel = Channel(channel_name)
message = Message(type='error',
title='Error on experiment ' + exp_name,
message=str(exc))
message.send_to(channel)
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, exp_id, script, parameters, input_files,\
experiment_entity, platform_entity, sample_entity, channel_name, view, operation = args
channel = Channel(channel_name)
message = Message(type='error',
title='Error running ' + os.path.basename(script),
message=str(exc))
message.send_to(channel)
def func_wrapper(*args, **kwargs):
try:
return func(*args, **kwargs)
except Exception as e:
error_msg = Message(type='error',
title='Error',
message=str(e) + '<br>' +
traceback.format_exc())
return HttpResponse(json.dumps(error_msg.to_dict()),
content_type="application/json")
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, file_path, bio_feature_name, file_type, channel_name, view, operation = args
channel = Channel(channel_name)
message = Message(type='error', title='Error', message=str(exc))
message.send_to(channel)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
log = MessageLog()
log.title = "Importing " + bio_feature_name + " (biological features) from " + file_type + " file"
log.message = "Status: error, File: " + os.path.basename(file_path) + ", Type: " + file_type + \
", Task: " + task_id + ", User: "******"Exception: " + str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, plt_dir, platform_id, blast_file_name, alignment_length_1, gap_open_1, \
mismatches_1, alignment_length_2, gap_open_2, mismatches_2, channel_name, view, operation = args
channel = Channel(channel_name)
message = Message(type='error', title='Error', message=str(exc))
message.send_to(channel)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
platform = Platform.objects.using(
compendium.compendium_nick_name).get(id=platform_id)
log = MessageLog()
log.title = "Filtering of alignment " + blast_file_name
log.message = "Status: error, Platform: " + platform.platform_access_id + ", Alignment: " + blast_file_name + \
", Task: " + task_id + ", User: "******"Exception: " + str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
def on_success(self, retval, task_id, args, kwargs):
user_id, compendium_id, experiment_id, channel_name, view, operation = args
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': 'experiments',
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
compendium = CompendiumDatabase.objects.get(id=compendium_id)
exp = ExperimentSearchResult.objects.using(
compendium.compendium_nick_name).get(id=experiment_id)
log = MessageLog()
log.title = "Download experiment " + exp.experiment_access_id
log.message = "Status: success, Experiment: " + exp.experiment_access_id + ", Task: " + task_id + "," \
"User: "******"Notes: " + retval
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
if retval:
channel = Channel(channel_name)
message = Message(
type='info',
title='Download notes',
message="Duplicated samples are not imported! <br><br>" +
retval)
message.send_to(channel)
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, experiment_id, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
new_status = Status.objects.using(
compendium.compendium_nick_name).get(name='experiment_new')
exp = ExperimentSearchResult.objects.using(
compendium.compendium_nick_name).get(id=experiment_id)
exp.status = new_status
exp.save(using=compendium.compendium_nick_name)
log = MessageLog()
log.title = "Download experiment " + exp.experiment_access_id
log.message = "Status: error, Experiment: " + exp.experiment_access_id + ", Task: " + task_id + ", User: "******"Exception: " + str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
message = Message(type='error',
title='Error on experiment ' +
exp.experiment_access_id,
message=str(exc))
message.send_to(channel)
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': 'experiments',
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, plt_dir, platform_id, use_short_blastn, alignment_identity, \
channel_name, view, operation = args
channel = Channel(channel_name)
message = Message(type='error', title='Error', message=str(exc))
message.send_to(channel)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
platform = Platform.objects.using(
compendium.compendium_nick_name).get(id=platform_id)
log = MessageLog()
log.title = "Alignment of platform " + platform.platform_access_id
log.message = "Status: error, Platform: " + platform.platform_access_id + \
", Task: " + task_id + ", User: "******"Exception: " + str(exc) + ", Stacktrace: " + einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
blast_file_name = os.path.join(plt_dir, task_id + '.blast')
mapper = MicroarrayMapper(blast_file_name)
mapper.set_alignment_status('error')
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
# remove files
for file in [
f for f in os.listdir(plt_dir)
if os.path.isfile(os.path.join(plt_dir, f))
and f.startswith(task_id)
]:
if file.endswith('.sqlite') or file.endswith('.blast'):
continue
os.remove(os.path.join(plt_dir, file))
def func_wrapper(*args, **kwargs):
channel_name, view, request, user = args
channel = Channel(channel_name)
try:
func(*args, **kwargs)
except ProgrammingError as e:
error_msg = Message(type='error',
title='Error',
message=str(e) +
"<br><br> Is the compendium initialized?")
error_msg.send_to(channel)
except Exception as e:
error_msg = Message(type='error', title='Error', message=str(e))
error_msg.send_to(channel)
def export_raw_data(request, *args, **kwargs):
comp_id = request.POST['compendium_id']
channel_name = request.session['channel_name']
view = request.POST['view']
operation = request.POST['operation']
compendium = CompendiumDatabase.objects.get(id=comp_id)
base_dir = AdminOptions.objects.get(
option_name='raw_data_directory').option_value
full_dir = os.path.join(base_dir, compendium.compendium_nick_name,
'export_raw_data')
# check genes, raw_data and mapping
bio_features_check = BioFeature.objects.using(
compendium.compendium_nick_name).count() > 0
raw_data_check = RawData.objects.using(
compendium.compendium_nick_name).count() > 0
mapping_check = BioFeatureReporter.objects.using(compendium.compendium_nick_name).\
exclude(bio_feature__isnull=True).count() > 0
if bio_features_check and raw_data_check and mapping_check:
export_data.export_raw_data.apply_async(
(request.user.id, comp_id, full_dir, channel_name, view,
operation))
return HttpResponse(json.dumps({'success': True}),
content_type="application/json")
else:
error_msg = Message(type='error',
title='Cannot export data',
message='To export data you need to:'
'<ul>'
'<li>import biological features;</li>'
'<li>import at least one experiment;</li>'
'<li>platform mapped (if requested);</li>'
'</ul>')
return HttpResponse(json.dumps(error_msg.to_dict()),
content_type="application/json")
def func_wrapper(*args, **kwargs):
request = args[0]
if type(request) == str:
user = args[-1]
request = args[-2]
comp_id = request['compendium_id']
else:
user = request.user
if 'compendium_id' in request.POST:
comp_id = request.POST['compendium_id']
else:
comp_id = json.loads(
request.POST['request'])['compendium_id']
if user.is_staff and user.is_superuser:
return func(*args, **kwargs)
compendium = CompendiumDatabase.objects.get(id=comp_id)
for g in user.groups.all():
for p in g.permissions.all():
if p.content_type.app_label == compendium.compendium_nick_name and p.codename == perm_codename:
return func(*args, **kwargs)
error_msg = Message(type='permission_error', title='', message='')
return HttpResponse(json.dumps(error_msg.to_dict()),
content_type="application/json")
def on_success(self, retval, task_id, args, kwargs):
user_id, compendium_id, experiment_id, keep_platform, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
exp = Experiment.objects.using(compendium.compendium_nick_name).get(id=experiment_id)
parsing_db = init_parsing(compendium_id, experiment_id)
report = retval
log = MessageLog()
log.title = "Experiment: " + exp.experiment_access_id + " imported"
log.message = "Status: success, Experiment: " + exp.experiment_access_id + ", Task: " + task_id + ", User: "******" Results: " + report
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
# delete CSV files
try:
for fl in glob.glob(parsing_db + '*.csv'):
os.remove(fl)
except Exception as e:
pass
message = Message(type='info', title='Successfully imported experiment',
message='Successfully imported experiment ' + exp.experiment_access_id +
'<br>' + report
)
message.send_to(channel)
imported_status = Status.objects.using(compendium.compendium_nick_name).get(name='experiment_raw_data_imported')
exp.status = imported_status
exp.save(using=compendium.compendium_nick_name)
Group("compendium_" + str(compendium_id) + "_" + str(experiment_id)).send({
'text': json.dumps({
'stream': view,
'payload': {
'request': {'operation': 'refresh'},
'data': None
}
})
})
def on_success(self, retval, task_id, args, kwargs):
user_id, compendium_id, experiment_id, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
exp = Experiment.objects.using(compendium.compendium_nick_name).get(id=experiment_id)
parsing_db = init_parsing(compendium_id, experiment_id)
platforms = [plt.platform_access_id for plt in ParsingPlatform.objects.using(parsing_db).all()]
log = MessageLog()
log.title = "Platforms: " + ", ".join(platforms) + " imported"
log.message = "Status: success, Platforms: " + ", ".join(platforms) + ", Experiment: " + \
exp.experiment_access_id + ", Task: " + task_id + ", User: "******" Results: " + retval
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
# delete CSV file
for fl in glob.glob(parsing_db + '*bio_feature*.csv'):
os.remove(fl)
message = Message(type='info', title='Successfully imported platforms',
message='Successfully imported platforms for experiment ' + exp.experiment_access_id +
' (' + ','.join(platforms) + ') <br>' + retval
)
message.send_to(channel)
ready_status = Status.objects.using(compendium.compendium_nick_name).get(name='platform_imported')
for parsing_platform in ParsingPlatform.objects.using(parsing_db).all():
plt = Platform.objects.using(compendium.compendium_nick_name).get(id=parsing_platform.platform_fk)
plt.status = ready_status
plt.save(using=compendium.compendium_nick_name)
Group("compendium_" + str(compendium_id) + "_" + str(experiment_id)).send({
'text': json.dumps({
'stream': view,
'payload': {
'request': {'operation': 'refresh'},
'data': None
}
})
})
def on_success(self, retval, task_id, args, kwargs):
user_id, compendium_id, exp_id, entity_type, entity_id, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
exp = Experiment.objects.using(
compendium.compendium_nick_name).get(id=exp_id)
parsed_status = Status.objects.using(
compendium.compendium_nick_name).get(name='entity_script_parsed')
entity_access_id = ''
if entity_type == 'experiment':
entity_access_id = exp.experiment_access_id
for af in exp.assignedfile_set.all():
log = MessageLog()
log.title = exp.experiment_access_id + " " + af.script_name + " completed on file " + af.input_filename
log.message = "Status: success, Experiment: " + exp.experiment_access_id + ", Order: " + str(
af.order) + ", Parameters: " + " ".join(
af.parameters
) + " Task: " + task_id + ", User: "******" " + af.script_name + " completed on file " + af.input_filename
log.message = "Status: success, Platform: " + platform.platform_access_id + ", Order: " + str(
af.order) + ", Parameters: " + " ".join(
af.parameters
) + " Task: " + task_id + ", User: "******" " + af.script_name + " completed on file " + af.input_filename
log.message = "Status: success, Sample: " + sample.sample_name + ", Order: " + str(
af.order) + ", Parameters: " + " ".join(
af.parameters
) + " Task: " + task_id + ", User: "******"compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'parse_experiment_platform',
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'message_log',
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'file_assignment_list',
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
if retval:
message = Message(type='parsing_log',
title='Parsing STDOUT ' + entity_type + ' ' +
entity_access_id + ', experiment: ' +
exp.experiment_access_id,
message=retval.replace('\n', '<br>'))
message.send_to(channel)
def on_failure(self, exc, task_id, args, kwargs, einfo):
user_id, compendium_id, exp_id, entity_type, entity_id, channel_name, view, operation = args
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
exp = Experiment.objects.using(
compendium.compendium_nick_name).get(id=exp_id)
error_status = Status.objects.using(
compendium.compendium_nick_name).get(name='entity_script_error')
access_id = ''
if entity_type == 'experiment':
for af in exp.assignedfile_set.all():
log = MessageLog()
log.title = exp.experiment_access_id + " " + af.script_name + " error on file " + af.input_filename
log.message = "Status: error, Experiment: " + exp.experiment_access_id + ", Order: " + str(
af.order) + ", Parameters: " + " ".join(
af.parameters) + " Task: " + task_id + ", User: "******", Exception: " + str(exc) + ", Stacktrace: " + \
einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
af.status = error_status
af.message_log = log
af.save(using=compendium.compendium_nick_name)
elif entity_type == 'platform':
platform = Platform.objects.using(
compendium.compendium_nick_name).get(id=entity_id)
for af in platform.assignedfile_set.all():
log = MessageLog()
log.title = exp.experiment_access_id + " " + af.script_name + " error on file " + af.input_filename
log.message = "Status: error, Platform: " + platform.platform_access_id + ", Order: " + str(
af.order) + ", Parameters: " + " ".join(
af.parameters) + " Task: " + task_id + ", User: "******", Exception: " + str(exc) + ", Stacktrace: " + \
einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
af.status = error_status
af.message_log = log
af.save(using=compendium.compendium_nick_name)
elif entity_type == 'sample':
sample = Sample.objects.using(compendium.compendium_nick_name).get(
experiment=exp, id=entity_id)
access_id = sample.sample_name
for af in sample.assignedfile_set.all():
log = MessageLog()
log.title = exp.experiment_access_id + " " + af.script_name + " error on file " + af.input_filename
log.message = "Status: error, Sample: " + sample.sample_name + ", Order: " + str(
af.order) + ", Parameters: " + " ".join(
af.parameters) + " Task: " + task_id + ", User: "******", Exception: " + str(exc) + ", Stacktrace: " + \
einfo.traceback
log.source = log.SOURCE[1][0]
log.save(using=compendium.compendium_nick_name)
af.status = error_status
af.message_log = log
af.save(using=compendium.compendium_nick_name)
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'message_log',
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'file_assignment',
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
message = Message(type='error',
title='Error parsing ' + entity_type + ' ' +
access_id,
message=str(exc))
message.send_to(channel)
def experiment_public_download(self, user_id, compendium_id, experiment_id,
channel_name, view, operation):
init_database_connections()
channel = Channel(channel_name)
user = User.objects.get(id=user_id)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
task_id = self.request.id
operation = operation + "_" + str(experiment_id)
downloading_status = Status.objects.using(
compendium.compendium_nick_name).get(name='experiment_downloading')
exp = ExperimentSearchResult.objects.using(
compendium.compendium_nick_name).get(id=experiment_id)
exp.status = downloading_status
exp.save(using=compendium.compendium_nick_name)
try:
ViewTask.objects.using(compendium.compendium_nick_name). \
get(operation=operation, view=view).delete()
except Exception as e:
pass
channel_task = ViewTask(task_id=task_id, operation=operation, view=view)
channel_task.save(using=compendium.compendium_nick_name)
data_ready_status = Status.objects.using(
compendium.compendium_nick_name).get(name='experiment_data_ready')
base_output_directory = AdminOptions.objects.get(
option_name='download_directory')
exp = ExperimentSearchResult.objects.using(
compendium.compendium_nick_name).get(id=experiment_id)
out_dir = os.path.join(base_output_directory.option_value,
compendium.compendium_nick_name,
exp.experiment_access_id)
os.makedirs(out_dir, exist_ok=True)
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
log_message = ''
module_name, class_name = '.'.join(exp.data_source.python_class.split('.')[:-1]), \
exp.data_source.python_class.split('.')[-1]
python_class = getattr(importlib.import_module(module_name), class_name)()
python_class.download_experiment_files(exp.experiment_access_id,
user.email, out_dir)
try:
Experiment.objects.using(compendium.compendium_nick_name).get(
experiment_access_id=exp.experiment_access_id)
message = Message(
type='info',
title='Experiment already exists',
message='The experiment ' + exp.experiment_access_id +
' is already present in the database. Data have been download anyway.'
)
message.send_to(channel)
except Exception as e:
log_message = python_class.create_experiment_structure(
compendium_id, experiment_id, out_dir)
exp.status = data_ready_status
exp.save(using=compendium.compendium_nick_name)
return log_message
def on_success(self, retval, task_id, args, kwargs):
user_id, compendium_id, plt_dir, platform_id, filter_id, \
blast_file_name, channel_name, view, operation = args
csv_file, without_mapping_before, with_mapping_before = retval
without_mapping_before = set(without_mapping_before)
channel = Channel(channel_name)
compendium = CompendiumDatabase.objects.get(id=compendium_id)
without_mapping_after = set(
BioFeatureReporter.objects.using(
compendium.compendium_nick_name).filter(
platform_id=platform_id,
bio_feature__isnull=True).values_list(
'id', flat=True).distinct())
with_mapping_after = dict(
BioFeatureReporter.objects.using(
compendium.compendium_nick_name).filter(
platform_id=platform_id,
bio_feature__isnull=False).values_list(
'id', 'bio_feature_id'))
added = len(
set.intersection(without_mapping_before,
set(with_mapping_after.keys())))
removed = len(
set.intersection(set(with_mapping_before.keys()),
without_mapping_after))
changed = len(set.intersection(set(with_mapping_before.keys()), set(with_mapping_after.keys()))) - \
len(set.intersection(set(with_mapping_before.items()), set(with_mapping_after.items())))
unchanged_mapped = len(
set.intersection(set(with_mapping_before.items()),
set(with_mapping_after.items())))
unchanged_unmapped = len(
set.intersection(without_mapping_before, without_mapping_after))
report = 'added: {}, removed: {}, changed: {}, unchanged_mapped: {}, unchanged_unmapped: {}'.format(
added, removed, changed, unchanged_mapped, unchanged_unmapped)
plt = Platform.objects.using(
compendium.compendium_nick_name).get(id=platform_id)
log = MessageLog()
log.title = "Platform: " + plt.platform_access_id + " mapping imported"
log.message = "Status: success, Platform: " + plt.platform_access_id +\
", Report: " + report + ", Task: " + task_id + ", User: "******"/*.blast"):
mapper = MicroarrayMapper(os.path.join(plt_dir, blast_file))
mapper.set_imported(False)
mapper = MicroarrayMapper(os.path.join(plt_dir, blast_file_name))
mapper.set_imported(True, filter_id)
mapper.set_filter_status(filter_id, 'ready')
Group("compendium_" + str(compendium_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
def on_success(self, retval, task_id, args, kwargs):
user_id, compendium_id, exp_id, script, parameters, input_files,\
experiment_entity, platform_entity, sample_entity, channel_name, view, operation = args
channel = Channel(channel_name)
message = Message(type='info',
title='Assigned script run succesfully.',
message=retval[0])
message.send_to(channel)
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'experiment_' + view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'platform_' + view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
Group("compendium_" + str(compendium_id) + "_" + str(exp_id)).send({
'text':
json.dumps({
'stream': 'sample_' + view,
'payload': {
'request': {
'operation': 'refresh'
},
'data': None
}
})
})
if retval[1]:
message = Message(type='parsing_log',
title='Assignment script',
message=retval[1].replace('\n', '<br>'))
message.send_to(channel)
def init_compendium(request, *args, **kwargs):
init_compendium.init_compendium(request.POST['values'])
init_database_connections()
msg = Message(type='info', title='Compendium initialized', message='Compendium successfully initialized')
return HttpResponse(json.dumps(msg.to_dict()),
content_type="application/json")