def data_paste(request, uid):
"""Used to paste objects in results and data clipboards as a Data object."""
project = Project.objects.filter(uid=uid).first()
owner = request.user
board = request.GET.get("board")
clipboard = request.session.get(settings.CLIPBOARD_NAME, {})
data_clipboard = clipboard.get(board, [])
for datauid in data_clipboard:
if board == const.COPIED_DATA:
obj = Data.objects.filter(uid=datauid).first()
dtype = obj.type
else:
obj = Job.objects.filter(uid=datauid).first()
dtype = "DATA"
if obj:
auth.create_data(project=project,
path=obj.get_data_dir(),
user=owner,
name=obj.name,
type=dtype,
text=obj.text)
clipboard[board] = []
request.session.update({settings.CLIPBOARD_NAME: clipboard})
return redirect(reverse("data_list", kwargs=dict(uid=project.uid)))
def handle(self, *args, **options):
# Collect the parameters.
pid = options['pid']
did = options['did']
path = options['path']
update_toc = options["update"]
text = options['text']
name = options['name']
type = options['type']
data = Data.objects.get_all(uid=did).first()
# Work with existing data.
if data:
if update_toc:
data.make_toc()
print(f"*** Data id : {did} table of contents updated.")
return
project = Project.objects.filter(uid=pid).first()
# Project must exist.
if not project:
logger.error(f"Project uid={pid} not found!")
return
# Slightly different course of action on file and directories.
isfile = os.path.isfile(path)
isdir = os.path.isdir(path)
# The data field is empty.
if not (isfile or isdir):
logger.error(f"Path is not a file nor a directory: {path}")
return
# Generate alternate names based on input directory type.
print(f"*** Project: {project.name} ({project.uid})")
if isdir:
print(f"*** Linking directory: {path}")
altname = os.path.split(path)[0].split(os.sep)[-1]
else:
print(f"*** Linking file: {path}")
altname = os.path.split(path)[-1]
# Select the name.
name = name or altname
print(f"*** Creating data: {name}")
# Create the data.
auth.create_data(project=project,
path=path,
type=type,
name=name,
text=text)
def file_paste(request, uid):
project = Project.objects.filter(uid=uid).first()
clipboard = request.session.get(settings.CLIPBOARD_NAME, {})
file_clipboard = clipboard.get(const.COPIED_FILES, [])
for single_file in file_clipboard:
if os.path.exists(single_file):
auth.create_data(project=project, path=single_file, user=request.user)
clipboard[const.COPIED_FILES] = []
request.session.update({settings.CLIPBOARD_NAME: clipboard})
return redirect(reverse("data_list", kwargs=dict(uid=project.uid)))
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 test_add_data(self):
"Test adding data directory to a project using management commands "
data_directory = auth.join(__file__, "..", "data")
data = auth.create_data(project=self.project, path=data_directory)
self.assertTrue(os.path.exists(data.get_data_dir()), "Directory not being linked")
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.project.save()
# Set up generic data for editing
self.data = auth.create_data(project=self.project, path=__file__, name="tested")
def create_data(root_dir, data_list):
"""Create data from data list, paths are relative to root """
for data in data_list:
pid = data.get("project_uid", None)
# Get data path relative to root_dir
path = data.get("value", "")
project = Project.objects.get_all(uid=pid).first()
dtype = data.get("type")
text = data.get("help")
name = data.get("name")
path = path if path.startswith("/") else os.path.join(root_dir, path)
print(f"*** Creating data in project={pid}, path={path}")
# Create the data.
auth.create_data(project=project,
path=path,
type=dtype,
name=name,
text=text)
return
def test_dynamic_field(self):
"Test data generator"
from biostar.recipes import const
data = auth.create_data(self.project, path=__file__)
display_type = const.DROPDOWN
json_data = dict(display=display_type, value=data.name,
source= 'PROJECT')
field = factory.dynamic_field(json_data, project=self.project)
if not field:
self.assertFalse(f"field generator for display={display_type} failed")
