def recipe_run(request, uid):
"""
View used to execute recipes and start a 'Queued' job.
"""
recipe = Analysis.objects.filter(uid=uid).first()
# Form submission.
if request.method == "POST":
form = forms.RecipeInterface(request=request,
analysis=recipe,
json_data=recipe.json_data,
data=request.POST,
files=request.FILES)
# The form validation will authorize the job.
if form.is_valid():
# Create the job from the recipe and incoming json data.
#print(form.cleaned_data)
job = auth.create_job(analysis=recipe,
user=request.user,
fill_with=form.cleaned_data)
# Spool via UWSGI or start it synchronously.
tasks.execute_job.spool(job_id=job.id)
url = reverse("recipe_view",
kwargs=dict(uid=recipe.uid)) + "#results"
return redirect(url)
else:
messages.error(request, form.errors)
url = reverse("recipe_view", kwargs=dict(uid=recipe.uid)) + "#run"
return redirect(url)
def job_rerun(request, uid):
# Get the job.
job = Job.objects.filter(uid=uid).first()
next = request.GET.get('next')
# Get the recipe
recipe = job.analysis
# Get the job JSON
json_data = job.json_data
# Validate users can run the recipe.
valid, msg = auth.validate_recipe_run(user=request.user, recipe=recipe)
if not valid:
messages.error(request, msg)
redir = next or reverse('job_view', kwargs=dict(uid=job.uid))
return redirect(redir)
# Create a new job
job = auth.create_job(analysis=recipe,
user=request.user,
json_data=json_data)
# Spool via UWSGI or run it synchronously.
tasks.execute_job.spool(job_id=job.id)
return redirect(reverse('job_list', kwargs=dict(uid=job.project.uid)))
def recipe_run(request, uid):
"""
View used to execute recipes and start a 'Queued' job.
"""
analysis = Analysis.objects.filter(uid=uid).first()
project = analysis.project
# Form submission.
if request.method == "POST":
form = forms.RecipeInterface(request=request, analysis=analysis, json_data=analysis.json_data,
data=request.POST, files=request.FILES)
# The form validation will authorize the job.
if form.is_valid():
# Create the job from the recipe and incoming json data.
job = auth.create_job(analysis=analysis, user=request.user, fill_with=form.cleaned_data)
# Spool the job right away if UWSGI exists.
if tasks.HAS_UWSGI:
# Spool via UWSGI.
tasks.execute_job.spool(job_id=job.id)
return redirect(reverse("job_list", kwargs=dict(uid=project.uid)))
else:
initial = dict(name=f"Results for: {analysis.name}")
form = forms.RecipeInterface(request=request, analysis=analysis, json_data=analysis.json_data, initial=initial)
is_runnable = auth.authorize_run(user=request.user, recipe=analysis)
context = dict(project=project, analysis=analysis, form=form, is_runnable=is_runnable, activate='Run Recipe')
context.update(get_counts(project))
return render(request, 'recipe_run.html', context)
def setUp(self):
logger.setLevel(logging.WARNING)
self.username = f"tested{get_uuid(10)}"
self.owner = models.User.objects.create(username=self.username,
is_staff=True,
email="*****@*****.**")
self.owner.set_password("tested")
self.owner.save()
self.project = auth.create_project(user=self.owner,
name="Test project",
privacy=models.Project.PUBLIC,
uid="tested")
data = auth.create_data(project=self.project, path=__file__)
analysis = auth.create_analysis(project=self.project,
json_text='',
template="# Add code here.")
self.job = auth.create_job(analysis=analysis)
self.proj_params = dict(uid=self.project.uid)
self.analysis_params = dict(uid=analysis.uid)
self.recipes_id_param = dict(id=analysis.id)
self.data_params = dict(uid=data.uid)
self.job_params = dict(uid=self.job.uid)
self.data_file_params = dict(uid=data.uid, path="foo.txt")
self.job_file_params = dict(uid=self.job.uid, path="foo.txt")
def setUp(self):
logger.setLevel(logging.WARNING)
# Set up generic owner
self.owner = models.User.objects.create_user(
username=f"tested{get_uuid(10)}", email="*****@*****.**")
self.owner.set_password("tested")
self.project = auth.create_project(user=self.owner,
name="tested",
text="Text",
summary="summary",
uid="tested")
self.recipe = auth.create_analysis(project=self.project,
json_text="{}",
template="",
security=models.Analysis.AUTHORIZED)
self.snippet_type = models.SnippetType.objects.create(
name='Snippet type', owner=self.owner)
self.snippet = models.Snippet.objects.create(
command='ls -l',
type=self.snippet_type,
help_text='List files in directory',
owner=self.owner)
self.job = auth.create_job(analysis=self.recipe, user=self.owner)
self.job.save()
def test_scheduler(self):
"""
Test task scheduler used to run queued jobs.
"""
from biostar.recipes.tasks import scheduler
self.job = auth.create_job(analysis=self.recipe, user=self.owner)
self.job.state = models.Job.QUEUED
self.job.save()
def create_job(recipe):
"""Create a queued job for a recipe"""
json_data = recipe.json_data
# Get the data if it exists
for key, obj in json_data.items():
if obj.get("source") != "PROJECT":
continue
name = obj.get('value', '')
data = Data.objects.filter(project=recipe.project, name=name).first()
if not data:
logger.error(
f"Job not created! Missing data:{name} in analysis:{recipe.name}"
)
return
data.fill_dict(obj)
auth.create_job(analysis=recipe, json_data=json_data)
return
def setUp(self):
logger.setLevel(logging.WARNING)
# Set up generic owner
self.owner = models.User.objects.create_user(username=f"tested{util.get_uuid(10)}", email="*****@*****.**")
self.owner.set_password("tested")
self.project = auth.create_project(user=self.owner, name="tested", text="Text", summary="summary",
uid="tested")
self.recipe = auth.create_analysis(project=self.project, json_text="{}", template="",
security=models.Analysis.AUTHORIZED)
self.job = auth.create_job(analysis=self.recipe, user=self.owner)
self.job.save()
def handle(self, *args, **options):
json = options['json']
pid = options['id']
uid = options["uid"]
template_fname = options['template']
jobs = options['jobs']
update = options["update"]
verbosity = int(options['verbosity'])
if verbosity > 1:
logger.setLevel(logging.DEBUG)
logger.info(f"level={verbosity}")
# Require JSON and templates to exist.
if not (json and template_fname):
logger.error(
"This command requires --json and a --template to be set")
return
# Get the target project.
if pid:
project = Project.objects.filter(id=pid).first()
else:
project = Project.objects.filter(uid=uid).first()
# Invalid project specified.
if not project:
logger.error(f'No project with id={pid} , uid={uid}')
return
# JSON file does not exist.
if not os.path.isfile(json):
logger.error(f'No file found for --json={json}')
return
# Template file does not exist.
if not os.path.isfile(template_fname):
logger.error(f'No file found for --template={template_fname}')
return
try:
# Parse the json_text into json_data
json_text = open(json).read()
json_path = os.path.dirname(json)
json_data = hjson.loads(json_text)
except Exception as exc:
logger.exception(f"JSON exception in file: {json}\n{exc}")
return
try:
# Read the specification
template = open(template_fname).read()
except Exception as exc:
logger.exception(f"Template exception: {exc}")
return
try:
name = json_data.get("settings", {}).get("name", "")
text = json_data.get("settings", {}).get("help", "")
uid = json_data.get("settings", {}).get("uid", "")
image = json_data.get("settings", {}).get("image", "")
text = textwrap.dedent(text)
summary = json_data.get("settings", {}).get("summary", "")
analysis = auth.create_analysis(project=project,
uid=uid,
json_text=json_text,
summary=summary,
template=template,
name=name,
text=text,
security=Analysis.AUTHORIZED,
update=update)
# Load the image if specified.
if image:
image_path = os.path.join(json_path, image)
if os.path.isfile(image_path):
stream = open(image_path, 'rb')
analysis.image.save(image, stream, save=True)
logger.info(f"Image path: {image_path}")
else:
logger.error(f"Skipping invalid image path: {image_path}")
if jobs:
# When creating a job automatically for data in projects
# it will try to match the value of the parameter to the data name.
missing_name = ''
for key, obj in json_data.items():
if obj.get("source") != "PROJECT":
continue
name = obj.get('value', '')
data = Data.objects.filter(project=project,
name=name).first()
if not data:
missing_name = name
break
data.fill_dict(obj)
if missing_name:
logger.error(
f"Job not created! Missing data:{missing_name} in analysis:{analysis.name}"
)
else:
auth.create_job(analysis=analysis, json_data=json_data)
except Exception as exc:
logger.exception(f"Error: {exc}")
return