class Dependency(db.EmbeddedDocument):
source = db.StringField(max_length=50, required=True)
source_condition = db.StringField(
max_length=50,
required=True,
choices=[(x, x) for x in ["display", "format", "value"]])
target_scope = db.StringField(max_length=50, required=True)
target_effect = db.StringField(max_length=150)
class User(db.Document, UserMixin):
email = db.StringField(unique=True, max_length=255)
password = db.StringField(required=True, max_length=255)
last_login_at = db.DateTimeField()
current_login_at = db.DateTimeField()
last_login_ip = db.StringField(max_length=100)
current_login_ip = db.StringField(max_length=100)
login_count = db.IntField()
active = db.BooleanField(default=True)
confirmed_at = db.DateTimeField()
roles = db.ListField(db.ReferenceField(Role), default=[])
class Argument(db.EmbeddedDocument):
name = db.StringField(required=True, max_length=50)
arg_type = db.StringField(
required=True,
max_length=50,
choices=[(x, x) for x in [
"None", "integer", 'float', "string", "input", "output", "stdin",
"stdout", "stderr"
]])
prefix = db.StringField(max_length=2)
prefix_long = db.StringField(max_length=50)
value = db.StringField(max_length=50)
file_format = db.StringField(max_length=50)
rank = db.IntField()
choices = db.StringField(max_length=50)
label = db.StringField(max_length=50)
description = db.StringField(max_length=50)
display = db.StringField(
choices=[(x, x) for x in ["show", "hide", "show in advanced"]])
min_occurrence = db.StringField(max_length=3)
max_occurrence = db.StringField(max_length=50)
property_bag = db.StringField(max_length=50)
@property
def safe_name(self):
return self.name.replace(' ', '_')
dependencies = db.ListField(db.EmbeddedDocumentField(Dependency))
def toRDF(self, node):
"""
serialize an argument in RDF triples.
"""
node.dcterms_title = self.name
if self.arg_type != "None":
node.clp_type = surf.ns.CLP[self.arg_type]
node.clp_hasPrefix = self.prefix
node.clp_hasLongPrefix = self.prefix_long
node.clp_value = self.value
node.clp_format = self.format
node.rank = self.rank
node.dcterms_label = self.label
node.dcterms_description = self.description
node.save()
def fromRDF(self, node):
pass
class Template(db.Document):
name = db.StringField(max_length=128, required=True)
platform = db.ListField(db.StringField())
path = db.StringField()
author = db.ReferenceField(User)
last_modified = db.DateTimeField()
class Role(db.Document, RoleMixin):
name = db.StringField(required=True, unique=True, max_length=80)
description = db.StringField(max_length=255)
class Tool(db.Document):
# meta data for house keeping
submitter = db.ReferenceField(User)
last_modified = db.DateTimeField()
is_public = db.BooleanField(default=False)
name = db.StringField(required=True, max_length=50)
description = db.StringField(max_length=100)
author = db.StringField(max_length=50)
email = db.EmailField()
version = db.StringField(max_length=50)
help_text = db.StringField()
os = db.StringField(choices=[(x, x)
for x in ["Linux", "Windows", "MaxOS"]])
grid_access_type = db.StringField(choices=[
(x, x) for x in ["-", "LFN", "URL"]
]) # TODO: where should this go?
grid_access_location = db.StringField(
max_length=250) # TODO: where should this go?
requirements = db.ListField(db.EmbeddedDocumentField(ToolRequirement))
command_line_interface = db.EmbeddedDocumentField(CommandLineInterface)
def toRDF(self, rdf_format='turtle'):
"""
TODO: The model is not stable yet. This method may not work.
"""
base_url = 'http://cli-mate.lumc.nl/data/definitions/default/%s#' % self.name
store = surf.Store(reader='rdflib',
writer='rdflib',
rdflib_store='IOMemory')
session = surf.Session(store)
# set up RDF classes.
CLPCommandLineProgram = session.get_class(
surf.ns.CLP.CommandLineProgram)
CLPExecutionRequirements = session.get_class(
surf.ns.CLP.ExecutionRequirements)
CLPSoftware = session.get_class(surf.ns.CLP.Software)
CLPArgument = session.get_class(surf.ns.CLP.Argument)
# set up main node.
command_line_program = CLPCommandLineProgram(base_url + self.name)
command_line_program.dcterms_label = self.name
command_line_program.dcterms_title = self.binary
command_line_program.dcterms_description = self.description
command_line_program.clp_hasVersion = self.version
command_line_program.dcterms_comment = self.help_text
command_line_program.save()
# set up execution requirements
execution_requirements = CLPExecutionRequirements(
base_url + 'execution_requirements')
command_line_program.clp_hasExecutionRequirements = execution_requirements
execution_requirements.clp_requiresOperationSystem = surf.ns.CLP.Linux # TODO
if self.interpreter != '(binary)':
execution_requirements.clp_interpreter = surf.ns.CLP[
self.interpreter]
if self.grid_access_type != '-':
execution_requirements.clp_gridAccessType = self.grid_access_type
execution_requirements.clp_gridID = self.grid_access_location
for req in self.requirements:
software = CLPSoftware(base_url + req.name)
software.dcterms_tile = req.name
software.clp_gridID = req.location
software.clp_softwareType = req.type
execution_requirements.clp_requiresSoftware = software
execution_requirements.save()
# add arguments
argument_list = []
for arg in self.arguments:
argument = Argument(**arg)
argument_node = CLPArgument(base_url + arg['name'])
argument.toRDF(argument_node)
argument_list.append(argument_node)
command_line_program.clp_hasArgument = argument_list
# add document metadata
Agent = session.get_class(surf.ns.FOAF['Agent'])
agent = Agent('http://climate.lumc.nl')
agent.dcterms_title = app.config['TITLE']
agent.dcterms_creator = app.config['AUTHOR']
agent.dcterms_hasVersion = app.config['VERSION']
agent.save()
Document = session.get_class(surf.ns.DCTERMS['Document'])
document = Document('')
document.dcterms_creator = agent
document.dcterms_created = datetime.utcnow()
document.rdfs_label = 'RDF definition of %s' % self.name
session.commit()
# prepare for serialization
graph = session.default_store.reader.graph
for prefix, url in ns_dict.items():
graph.bind(prefix.lower(), url)
graph.bind('', base_url)
return graph.serialize(format=rdf_format)
def toTarget(self, template):
now = datetime.isoformat(datetime.utcnow()) + "Z"
meta = {
'label': 'RDF definition of %s' % self.name,
'last_modified': self.last_modified if self.last_modified else now,
'version': "CLI-mate (version %0.1f)" % app.config['VERSION'],
'time': now
}
# pad meta data information for better display
for key in meta:
meta[key] = meta[key].ljust(75, ' ')
return template.render(data=self, meta=meta)
class CommandLineInterface(db.EmbeddedDocument):
command = db.StringField(required=True, max_length=50)
interpreter = db.StringField(choices=[(
x, x) for x in ["(binary)", "bash", "java", "perl", "python", "ruby"]])
arguments = db.ListField(db.EmbeddedDocumentField(Argument))
class ToolRequirement(db.EmbeddedDocument):
req_type = db.StringField(choices=[(x, x)
for x in ["binary", "python-module"]])
name = db.StringField(max_length=50),
location = db.StringField(max_length=200)