Merge pull request #207 from Galithil/master

Extended Researcher to handle Roles and Permissions.

Author: Hammarn

genologics/descriptors.py

@@ -164,7 +164,7 @@ def __init__(self, instance, *args, **kwargs):
 
     @property
     def rootnode(self):
-        if not self._rootnode:
+        if self._rootnode is None:
             self._rootnode = self.instance.root
             for rootkey in self.rootkeys:
                 self._rootnode = self._rootnode.find(rootkey)
@@ -431,6 +431,45 @@ def __get__(self, instance, cls):
 
         return result
 
+class NestedBooleanDescriptor(TagDescriptor):
+    def __init__(self, tag, *args):
+        super(NestedBooleanDescriptor, self).__init__(tag)
+        self.rootkeys = args
+
+    def __get__(self, instance, cls):
+        instance.get()
+        result = None
+        rootnode = instance.root
+        for rootkey in self.rootkeys:
+            rootnode = rootnode.find(rootkey)
+        result = rootnode.find(self.tag).text.lower() == 'true'
+        return result
+
+    def __set__(self, instance, value):
+        rootnode = instance.root
+        for rootkey in self.rootkeys:
+            rootnode = rootnode.find(rootkey)
+        rootnode.find(self.tag).text = str(value).lower()
+
+class NestedStringDescriptor(TagDescriptor):
+    def __init__(self, tag, *args):
+        super(NestedStringDescriptor, self).__init__(tag)
+        self.rootkeys = args
+
+    def __get__(self, instance, cls):
+        instance.get()
+        result = None
+        rootnode = instance.root
+        for rootkey in self.rootkeys:
+            rootnode = rootnode.find(rootkey)
+        result = rootnode.find(self.tag).text
+        return result
+
+    def __set__(self, instance, value):
+        rootnode = instance.root
+        for rootkey in self.rootkeys:
+            rootnode = rootnode.find(rootkey)
+        rootnode.find(self.tag).text = value
 
 class NestedAttributeListDescriptor(StringAttributeDescriptor):
     """An instance yielding a list of dictionnaries of attributes
@@ -514,6 +553,8 @@ def __get__(self, instance, cls):
         from genologics.entities import Container
         instance.get()
         node = instance.root.find(self.tag)
+        if node is None:
+            return (None,None)
         uri = node.find('container').attrib['uri']
         return Container(instance.lims, uri=uri), node.find('value').text
 
@@ -572,3 +613,4 @@ def get_dict(self, lims, node):
         if node is not None:
             result['parent-process'] = Process(lims, node.attrib['uri'])
         return result
+

genologics/entities.py

@@ -11,7 +11,8 @@
     UdtDictionaryDescriptor, ExternalidListDescriptor, EntityDescriptor, BooleanDescriptor, EntityListDescriptor, \
     StringAttributeDescriptor, StringListDescriptor, DimensionDescriptor, IntegerDescriptor, \
     PlacementDictionaryDescriptor, InputOutputMapList, LocationDescriptor, ReagentLabelList, NestedEntityListDescriptor, \
-    NestedStringListDescriptor, NestedAttributeListDescriptor, IntegerAttributeDescriptor
+    NestedStringListDescriptor, NestedAttributeListDescriptor, IntegerAttributeDescriptor, NestedStringDescriptor, \
+    NestedBooleanDescriptor
 
 try:
     from urllib.parse import urlsplit, urlparse, parse_qs, urlunparse
@@ -317,13 +318,26 @@ def _create(cls, lims, creation_tag=None, **kwargs):
     @classmethod
     def create(cls, lims, creation_tag=None, **kwargs):
         """Create an instance from attributes then post it to the LIMS"""
-        instance = cls._create(lims, creation_tag=None, **kwargs)
+        instance = cls._create(lims, creation_tag=creation_tag, **kwargs)
         data = lims.tostring(ElementTree.ElementTree(instance.root))
         instance.root = lims.post(uri=lims.get_uri(cls._URI), data=data)
         instance._uri = instance.root.attrib['uri']
         return instance
 
 
+class Instrument(Entity):
+    """Lab Instrument
+    """
+    _URI = "instruments"
+    _tag = "instrument"
+    _PREFIX = "inst"
+
+    name = StringDescriptor('name')
+    type = StringDescriptor('type')
+    serial_number = StringDescriptor('serial-number')
+    expiry_date = StringDescriptor('expiry-date')
+    archived = BooleanDescriptor('archived')
+
 class Lab(Entity):
     "Lab; container of researchers."
 
@@ -338,7 +352,6 @@ class Lab(Entity):
     externalids      = ExternalidListDescriptor()
     website          = StringDescriptor('website')
 
-
 class Researcher(Entity):
     "Person; client scientist or lab personnel. Associated with a lab."
 
@@ -357,11 +370,26 @@ class Researcher(Entity):
     externalids = ExternalidListDescriptor()
 
     # credentials XXX
+    username = NestedStringDescriptor('username', 'credentials')
+    account_locked = NestedBooleanDescriptor('account-locked', 'credentials')
 
     @property
     def name(self):
         return "%s %s" % (self.first_name, self.last_name)
 
+class Permission(Entity):
+    """A Clarity permission. Only supports GET"""
+    name = StringDescriptor('name')
+    action = StringDescriptor('action')
+    description = StringDescriptor('description')
+
+
+class Role(Entity):
+    """Clarity Role, hosting permissions"""
+    name = StringDescriptor('name')
+    researchers = NestedEntityListDescriptor('researcher', Researcher, 'researchers')
+    permissions = NestedEntityListDescriptor('permission', Permission, 'permissions')
+
 
 class Reagent_label(Entity):
     """Reagent label element"""
@@ -473,6 +501,9 @@ def get_placements(self):
         self.lims.get_batch(list(result.values()))
         return result
 
+    def delete(self):
+        self.lims.delete(self.uri)
+
 
 class Processtype(Entity):
     _TAG = 'process-type'
@@ -517,8 +548,8 @@ class Process(Entity):
     udt               = UdtDictionaryDescriptor()
     files             = EntityListDescriptor(nsmap('file:file'), File)
     process_parameter = StringDescriptor('process-parameter')
+    instrument        = EntityDescriptor('instrument', Instrument)
 
-    # instrument XXX
     # process_parameters XXX
 
     def outputs_per_input(self, inart, ResultFile=False, SharedResultFile=False, Analyte=False):
@@ -704,13 +735,14 @@ class StepPools(Entity):
     def _remove_available_inputs(self, input_art):
         """ removes an input from the available inputs, one replicate at a time
         """
+        self.get_available_inputs()
         rep = self._available_inputs.get(input_art, {'replicates': 0}).get('replicates', 1)
         if rep > 1:
             self._available_inputs[input_art]['replicates'] = rep - 1
         elif rep == 1:
             del(self._available_inputs[input_art])
         else:
-            raise Exception("No more replicates left for artifact {0}".format(input_art))
+            logger.info("using more inputs than replicates for input {0}".format(input_art.uri))
         self.available_inputs = self._available_inputs
 
     def set_available_inputs(self, available_inputs):
@@ -719,7 +751,7 @@ def set_available_inputs(self, available_inputs):
         for input_art in available_inputs:
             current_elem = ElementTree.SubElement(available_inputs_root, "input")
             current_elem.attrib['uri'] = input_art.uri
-            current_elem.attrib['replicates'] = available_inputs[input_art]['replicates']
+            current_elem.attrib['replicates'] = str(available_inputs[input_art]['replicates'])
         self._available_inputs = available_inputs
 
     def get_available_inputs(self):
@@ -784,7 +816,7 @@ def get_placement_list(self):
             for node in self.root.find('output-placements').findall('output-placement'):
                 input = Artifact(self.lims, uri=node.attrib['uri'])
                 location = (None, None)
-                if node.find('location'):
+                if node.find('location') is not None:
                     location = (
                         Container(self.lims, uri=node.find('location').find('container').attrib['uri']),
                         node.find('location').find('value').text
@@ -963,6 +995,7 @@ class Step(Entity):
     program_status     = EntityDescriptor('program-status', StepProgramStatus)
 
     def advance(self):
+        self.get()
         self.root = self.lims.post(
             uri="{}/advance".format(self.uri),
             data=self.lims.tostring(ElementTree.ElementTree(self.root))
@@ -1035,6 +1068,7 @@ def __init__(self, lims, uri=None, id=None):
                     if child.attrib.get("name") == "Sequence":
                         self.sequence = child.attrib.get("value")
 
+
 class Queue(Entity):
     """Queue of a given step"""
     _URI = "queues"
@@ -1049,4 +1083,5 @@ class Queue(Entity):
 Artifact.workflow_stages = NestedEntityListDescriptor('workflow-stage', Stage, 'workflow-stages')
 Step.configuration       = EntityDescriptor('configuration', ProtocolStep)
 StepProgramStatus.configuration = EntityDescriptor('configuration', ProtocolStep)
+Researcher.roles = NestedEntityListDescriptor('role', Role, 'credentials')
 

genologics/lims.py

@@ -157,6 +157,16 @@ def post(self, uri, data, params=dict()):
                                    'accept': 'application/xml'})
         return self.parse_response(r, accept_status_codes=[200, 201, 202])
 
+    def delete(self, uri, params=dict()):
+        """sends a DELETE to the given URI.
+        Return the response XML as an ElementTree.
+        """
+        r = requests.delete(uri, params=params,
+                          auth=(self.username, self.password),
+                          headers={'content-type': 'application/xml',
+                                   'accept': 'application/xml'})
+        return self.validate_response(r, accept_status_codes=[204])
+
     def check_version(self):
         """Raise ValueError if the version for this interface
         does not match any of the versions given for the API.
@@ -365,6 +375,13 @@ def get_artifacts(self, name=None, type=None, process_type=None,
         else:
             return self._get_instances(Artifact, params=params)
 
+    def get_container_types(self, name=None, start_index=None):
+        """Get a list of container types, filtered by keyword arguments.
+        name: Container Type name.
+        start-index: Page to retrieve, all if None."""
+        params = self._get_params(name=name, start_index=start_index)
+        return self._get_instances(Containertype, params=params)
+
     def get_containers(self, name=None, type=None,
                        state=None, last_modified=None,
                        udf=dict(), udtname=None, udt=dict(), start_index=None,
@@ -455,6 +472,11 @@ def get_reagent_lots(self, name=None, kitname=None, number=None,
                                   start_index=start_index)
         return self._get_instances(ReagentLot, params=params)
 
+    def get_instruments(self, name=None):
+        """Returns a list of Instruments, can be filtered by name"""
+        params = self._get_params(name=name)
+        return self._get_instances(Instrument, params=params)
+
     def _get_params(self, **kwargs):
         "Convert keyword arguments to a kwargs dictionary."
         result = dict()

genologics/version.py

@@ -1 +1 @@
-__version__="0.3.16"
+__version__="0.3.17"