diff --git a/pyKADMOS/sample/graph.py b/pyKADMOS/sample/graph.py
index 863c9d21f559240304d48f5d8139f62572201215..79b6f15798158af074e24cbf0879764c7789953e 100644
--- a/pyKADMOS/sample/graph.py
+++ b/pyKADMOS/sample/graph.py
@@ -10,6 +10,7 @@ import itertools
import filecmp
import time
import copy
+import ast
import shutil
import distutils.util
@@ -37,7 +38,7 @@ from pyKADMOS.sample.rce import RceWorkflow
from pyKADMOS.sample.utilities import transform_data_into_strings, transform_string_into_format, extend_list_uniquely,\
export_as_json, move_and_open, make_camel_case, unmake_camel_case, get_list_entries, open_file, Child, ChildGroup,\
recursively_empty, format_string_for_d3js, get_unique_friendly_id, ChildSequence, remove_if_exists,\
- recursively_stringify, make_plural
+ recursively_stringify, make_plural, recursively_dictify
from pyKADMOS.sample.utilities import color_list, test_attr_cond, hex_to_rgb
from pyKADMOS.sample import prompt_utilities as PRO
@@ -4144,6 +4145,27 @@ class KadmosGraph(nx.DiGraph):
if remove_after_compress:
shutil.rmtree(vispack_folder)
+ def expand_node(self, node_name, elements):
+ """
+ Function to expand and clean-up a certain element of a specific node when a _ui_d is given
+ """
+ # TODO: Edit docstring
+ # TODO: Add input assertions
+
+ for element in elements:
+ graph_element_name = make_plural(unmake_camel_case(element[0], '_'))
+ initial_element_data = self.node[node_name].get(graph_element_name)
+ if initial_element_data is not None:
+ for data_key, data_value in initial_element_data.iteritems():
+ for sub_data_key, sub_data_value in data_value.iteritems():
+ if sub_data_key.endswith('_ui_d'):
+ new_subelement_id = '/' + sub_data_value.split('/', 1)[1]
+ new_subelement_data = dict(zip(element[1], [self.node[new_subelement_id].get(e) for e in element[1]]))
+ self.node[node_name][graph_element_name][new_subelement_id] = new_subelement_data
+ del self.node[node_name][graph_element_name][data_key]
+
+ return self.node[node_name]
+
def load_from_cmdows(filename, source_folder=None, kadmos_check_critical=True):
"""
@@ -4296,19 +4318,35 @@ def load_from_cmdows(filename, source_folder=None, kadmos_check_critical=True):
# The following nodes and edges are only generated for MDGs
if isinstance(graph, MdaoDataGraph):
- for node, data in graph.nodes_iter(data=True):
- print node
- print data
-
- # TODO: First set up architecture
+ # Create architecture element nodes
cmdows_architecture_parameters = cmdows.find('architectureElements/parameters')
for cmdows_architecture_parameter in list(cmdows_architecture_parameters):
for cmdows_single_architecture_parameter in list(cmdows_architecture_parameter):
cmdows_uid = cmdows_single_architecture_parameter.get('uID')
- graph.add_node(cmdows_block.text,
+ key_dict = {'relatedParameterUID': 'related_to_schema_node'}
+ attr_dict = recursively_dictify(cmdows_single_architecture_parameter, key_dict)
+ graph.add_node(cmdows_uid,
+ attr_dict,
category='variable',
- related_to_schema_node = cmdows_single_architecture_parameter.findtext('relatedParamterUID'),
- label = cmdows_single_architecture_parameter.findtext('label'))
+ architecture_role=unmake_camel_case(cmdows_single_architecture_parameter.tag, ' '))
+ cmdows_architecture_exe_blocks = cmdows.find('architectureElements/executableBlocks')
+ for cmdows_architecture_exe_block in list(cmdows_architecture_exe_blocks):
+ for cmdows_single_architecture_exe_block in list(cmdows_architecture_exe_block):
+ cmdows_uid = cmdows_single_architecture_exe_block.get('uID')
+ if cmdows_uid is not None:
+ attr_dict = recursively_dictify(cmdows_single_architecture_exe_block)
+ graph.add_node(cmdows_uid,
+ attr_dict,
+ category='function',
+ architecture_role=cmdows_single_architecture_exe_block.tag)
+ # Copy node data from problem formulation to executableBlocks
+ graph.expand_node(cmdows_uid, graph.CMDOWS_ROLES_DEF)
+ else:
+ for role in graph.ARCHITECTURE_ROLES_FUNS:
+ cmdows_role_name = make_camel_case(role)
+ if cmdows_single_architecture_exe_block.tag == cmdows_role_name:
+ cmdows_uid = cmdows_single_architecture_exe_block.find('relatedExecutableBlockUID').text
+ graph.node[cmdows_uid]['architecture_role'] = role
# Create MDG edges
cmdows_data_graph = cmdows.find('workflow/dataGraph')
@@ -4318,6 +4356,10 @@ def load_from_cmdows(filename, source_folder=None, kadmos_check_critical=True):
for edge in list(cmdows_edges):
graph.add_edge(edge.findtext('fromUID'), edge.findtext('toUID'))
+ #for node, data in graph.nodes_iter(data=True):
+ # print node
+ # print data
+
# TODO: Make process graph
#print graph.graph
diff --git a/pyKADMOS/sample/utilities.py b/pyKADMOS/sample/utilities.py
index 1c4c0a9db69b57fd0a888a64e547b71318289787..0f3396576ddaa2268d0c48551c71487102d784a6 100644
--- a/pyKADMOS/sample/utilities.py
+++ b/pyKADMOS/sample/utilities.py
@@ -153,7 +153,7 @@ def get_mdao_setup(mdao_setup):
allow_unconverged_couplings = False
else:
raise IOError('Incorrect mdao_setup "%s" specified.' % mdao_setup)
- return mdo_architecture,mda_type,allow_unconverged_couplings
+ return mdo_architecture, mda_type, allow_unconverged_couplings
def test_attr_cond(attr_value, operator, test_value):
@@ -170,7 +170,7 @@ def test_attr_cond(attr_value, operator, test_value):
:rtype: bool
"""
# Assert inputs
- pos_ops = ['<','<=','==','!=','>=','>', 'in']
+ pos_ops = ['<', '<=', '==', '!=', '>=', '>', 'in']
assert isinstance(operator,str)
assert set([operator]).intersection(set(pos_ops)), "'%s' is an invalid operator, possible operators are: %s." % \
(operator, pos_ops)
@@ -246,8 +246,8 @@ def transform_data_into_strings(data, keys_to_be_removed=list()):
"""
# Input assertions
- assert isinstance(data,dict)
- assert isinstance(keys_to_be_removed,list)
+ assert isinstance(data, dict)
+ assert isinstance(keys_to_be_removed, list)
for key, item in data.iteritems():
if item is None:
@@ -345,8 +345,8 @@ def make_camel_case(string, make_plural_option=False):
:param string: non-camelcase string
:type string: str
- :param make_plural: pluralize camelcase string
- :type make_plural: bool
+ :param make_plural_option: pluralize camelcase string
+ :type make_plural_option: bool
:return: camelcase string
:rtype: str
"""
@@ -361,18 +361,20 @@ def make_camel_case(string, make_plural_option=False):
return string
-def unmake_camel_case(string):
+def unmake_camel_case(string, separator='_'):
"""
- Function to make camelCase a string with underscores.
+ Function to make camelCase a string with separator (e.g. underscores).
:param string: camelCase string
:type string: str
- :return: string with underscores
+ :param separator: symbol/symbols used as separator
+ :type string: str
+ :return: string with separator
:rtype: str
"""
- string = re.sub(r"(\w)([A-Z])", r"\1_\2", string) # Add underscores
- string = string.lower() # Remove capitalization
+ string = re.sub(r"(\w)([A-Z])", r"\1"+separator+r"\2", string) # Add separator
+ string = string.lower() # Remove capitalization
return string
@@ -476,7 +478,7 @@ def open_file(filename):
def Child(parent, tag, content='', attrib={}, **extra):
"""
- Utility function extending the xml.etree.ElementTree.SubElement function
+ Utility function extending the xml.etree.ElementTree.SubElement function.
:param parent: The parent element
:param tag: The subelement name
@@ -499,7 +501,7 @@ def Child(parent, tag, content='', attrib={}, **extra):
def ChildSequence(parent, data, data_keys=None, data_dict=None):
"""
Utility function extending the previously defined Child function such that sequences
- can easily be created in an xml.etree.ElementTree
+ can easily be created in an xml.etree.ElementTree.
:param parent: The parent element
:param data: The list of data to be written to the sequence in the form [[key1, value1], [key2, value2]]
@@ -562,13 +564,11 @@ def ChildGroup(graph, attr_name, attr_value, data_list):
for index in range(len(data_list)):
data_key = data_list[index][0]
data_value = data_list[index][1]
- # TODO: Remove if statement if all values from data_list need to be present
if graph.node[node].get(data_key) is not None:
if isinstance(data_value, list):
# For design variables and similar cases
subsubelement = Child(subelement, data_value[0])
- # TODO: If KADMOS allows for more than one objectiveVariable at some point
- # the fix below can be removed
+ # TODO: If KADMOS allows for more than one objectiveVariable at some point this fix can be removed
if data_value[0] == 'objectiveVariables':
graph.node[node][data_key] = {graph.node[node][data_key][0]: graph.node[node][data_key][0]}
for subdata_key, subdata_value in graph.node[node][data_key].iteritems():
@@ -602,7 +602,7 @@ def recursively_empty(e):
def recursively_stringify(tree):
"""
- Utility function to recursively stringify a ElementTree object (for file comparison)
+ Utility function to recursively stringify a ElementTree object (for file comparison).
:param tree: Input ElementTree object
:return: List of strings representing the ElementTree object
@@ -620,4 +620,45 @@ def recursively_stringify(tree):
string_list.sort()
- return string_list
\ No newline at end of file
+ return string_list
+
+
+def recursively_dictify(element, key_dict={}):
+ """
+ Utility function to recursively convert a ElementTree.Element object to a dictionary
+
+ :param element: Input ElementTree.Element
+ :param element: Dictionary for translating keys
+ :return: dictionary representing the ElementTree.Element
+ """
+
+ # Create dictionary
+ dictionary = {}
+
+ # Loop over element
+ for subelement in list(element):
+ # If subelement contains a string it is assumed that the final level of the dictionary is reached
+ if subelement.text.strip():
+ # Check if string is actually a list and convert to a list in this case
+ try:
+ subelement_value = ast.literal_eval(subelement.text)
+ if not isinstance(subelement_value, list):
+ raise ValueError
+ except (SyntaxError, ValueError) as e:
+ subelement_value = subelement.text.strip()
+ # If subelement contains other elements start recursive loop
+ elif list(subelement) is not None:
+ subelement_value = recursively_dictify(subelement)
+
+ # Write value to dictionary
+ if subelement_value:
+ subelement_key = key_dict.get(subelement.tag, unmake_camel_case(subelement.tag, '_'))
+ # Check that this dictionary entry does not exits yet
+ # If so add identifier
+ if dictionary.get(subelement_key) is not None:
+ subelement_key = subelement_key + '_' + \
+ str(sum([key.startswith(subelement_key) for key in dictionary.keys()]))
+ dictionary[subelement_key] = subelement_value
+
+ # Return
+ return dictionary
diff --git a/pyKADMOS/scripts/loadtest.py b/pyKADMOS/scripts/loadtest.py
index 6c5be917023304a69faa7154083cf46fb75adaa6..5ee2318e69d1778d945a2c029c7a6ec67068a58c 100644
--- a/pyKADMOS/scripts/loadtest.py
+++ b/pyKADMOS/scripts/loadtest.py
@@ -4,6 +4,7 @@ logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.DEBUG)
from pyKADMOS.sample.graph import load_from_cmdows
source_folder = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'sellarProblemRCE')
-graph = load_from_cmdows('MDAO_IDF.xml', source_folder=source_folder)
+#graph = load_from_cmdows('MDAO_IDF.xml', source_folder=source_folder)
+graph = load_from_cmdows('MDAO_converged-DOE-GS.xml', source_folder=source_folder)
#print graph.find_all_nodes()
\ No newline at end of file
diff --git a/pyKADMOS/scripts/sellarProblemRCE.py b/pyKADMOS/scripts/sellarProblemRCE.py
index cd9c5ee77ce2edde1704cac7b5fb4163e0f1e3b8..52c5e7d4b93ee281e2d1fb6e670bb81d4131f68a 100644
--- a/pyKADMOS/scripts/sellarProblemRCE.py
+++ b/pyKADMOS/scripts/sellarProblemRCE.py
@@ -38,7 +38,7 @@ from pyKADMOS.sample.utilities import get_mdao_setup
# Script settings
loop_all = False # Loop through all mdao_definition
-mdao_definition_id = 10 # If not loop_all = False, select the required MDAO architecture from mdao_definitions
+mdao_definition_id = 4 # If not loop_all = False, select the required MDAO architecture from mdao_definitions
open_pdfs = False # Automatically open PDFs of the (X)DSMs while running the script
pdfs_folder = 'sellarProblemRCE' # Subfolder to store the PDF in
script_rce_workflows = True # Set to True to script the RCE workflows
@@ -191,8 +191,8 @@ for mdao_definition in mdao_definitions:
MDG.plot_graph(11, color_setting='default', fig_size=fig_size, show_now=False)
# Save graph
- print MPG.find_all_nodes()
- print MPG.node['Gc']
+ print MDG.find_all_nodes()
+ print MDG.node['DOE']
MDG.save_as_cmdows('MDAO_'+mdao_definition, 'Test MDAO file', 'Imco van Gent', '0.1', MPG=MPG,
destination_folder=pdfs_folder, pretty_print=True)
#cmdows_integrity_check(MDG, MPG=MPG)
diff --git a/pyKADMOS/scripts/sellarProblemRCE/FPG.pdf b/pyKADMOS/scripts/sellarProblemRCE/FPG.pdf
index e7b2d3a99f8ac0f9d914e3a0346520b194412f52..d9e53046ca5422cc3f1bf7109a280dc1c85d9658 100644
Binary files a/pyKADMOS/scripts/sellarProblemRCE/FPG.pdf and b/pyKADMOS/scripts/sellarProblemRCE/FPG.pdf differ
diff --git a/pyKADMOS/scripts/sellarProblemRCE/FPG_converged-DOE-GS.xml b/pyKADMOS/scripts/sellarProblemRCE/FPG_converged-DOE-GS.xml
index ffbf9fb77b1e8df4e047d3ad6b0321f8a77c3ed7..d1121f828e2b4af8ec0aa871d3a35f3b75b8866b 100644
--- a/pyKADMOS/scripts/sellarProblemRCE/FPG_converged-DOE-GS.xml
+++ b/pyKADMOS/scripts/sellarProblemRCE/FPG_converged-DOE-GS.xml
@@ -3,14 +3,14 @@
<header>
<creator>Imco van Gent</creator>
<description>Test FPG file</description>
- <timestamp>2017-04-11T10:21:00.776000</timestamp>
+ <timestamp>2017-04-12T11:13:05.834000</timestamp>
<fileVersion>0.1</fileVersion>
<cmdowsVersion>0.4</cmdowsVersion>
<updates>
<update>
<modification>KADMOS export of a fundamental problem graph (FPG).</modification>
<creator>Imco van Gent</creator>
- <timestamp>2017-04-11T10:21:00.776000</timestamp>
+ <timestamp>2017-04-12T11:13:05.834000</timestamp>
<fileVersion>0.1</fileVersion>
<cmdowsVersion>0.4</cmdowsVersion>
</update>
diff --git a/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.pdf b/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.pdf
index 211023b429a566922a8fc67ffd26f92aa1633572..26dc01760af136070cf342de47a8ad4ddc83ab4d 100644
Binary files a/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.pdf and b/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.pdf differ
diff --git a/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.xml b/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.xml
index b8b98e66814a7767b7bec6f5ba6978fd359c20d7..3d19785139f4a7985ecc0a69b419b7b7b9979e66 100644
--- a/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.xml
+++ b/pyKADMOS/scripts/sellarProblemRCE/MDAO_converged-DOE-GS.xml
@@ -3,14 +3,14 @@
<header>
<creator>Imco van Gent</creator>
<description>Test MDAO file</description>
- <timestamp>2017-04-11T10:21:00.776000</timestamp>
+ <timestamp>2017-04-12T11:13:05.834000</timestamp>
<fileVersion>0.1</fileVersion>
<cmdowsVersion>0.4</cmdowsVersion>
<updates>
<update>
<modification>KADMOS Export of a mdao data graph (MDG) graph.</modification>
<creator>Imco van Gent</creator>
- <timestamp>2017-04-11T10:21:00.776000</timestamp>
+ <timestamp>2017-04-12T11:13:05.834000</timestamp>
<fileVersion>0.1</fileVersion>
<cmdowsVersion>0.4</cmdowsVersion>
</update>
diff --git a/pyKADMOS/scripts/sellarProblemRCE/RCG.pdf b/pyKADMOS/scripts/sellarProblemRCE/RCG.pdf
index db510f36054431c60bcf632db22a34db52295e77..325c4a6bcfe18b7dc9febbe5da639b1a200f9df4 100644
Binary files a/pyKADMOS/scripts/sellarProblemRCE/RCG.pdf and b/pyKADMOS/scripts/sellarProblemRCE/RCG.pdf differ
diff --git a/pyKADMOS/scripts/sellarProblemRCE/RCG.xml b/pyKADMOS/scripts/sellarProblemRCE/RCG.xml
index c96c0cd93923e44e8ce8099009a17987b13e3cd3..0d6c2fcd59caeea392994f84010b3fda288f9f24 100644
--- a/pyKADMOS/scripts/sellarProblemRCE/RCG.xml
+++ b/pyKADMOS/scripts/sellarProblemRCE/RCG.xml
@@ -3,14 +3,14 @@
<header>
<creator>Imco van Gent</creator>
<description>Test RCG file</description>
- <timestamp>2017-04-11T10:25:41.626000</timestamp>
+ <timestamp>2017-04-12T11:13:05.834000</timestamp>
<fileVersion>0.1</fileVersion>
<cmdowsVersion>0.4</cmdowsVersion>
<updates>
<update>
<modification>KADMOS export of a repository connectivity graph (RCG).</modification>
<creator>Imco van Gent</creator>
- <timestamp>2017-04-11T10:25:41.626000</timestamp>
+ <timestamp>2017-04-12T11:13:05.834000</timestamp>
<fileVersion>0.1</fileVersion>
<cmdowsVersion>0.4</cmdowsVersion>
</update>