Work in progress on CMDOWS functions

Former-commit-id: 6d17cb7dff64445bd0e35a1b276639fdb5889581

pyKADMOS/sample/graph.py

@@ -9,7 +9,6 @@ import sys
 import itertools
 import filecmp
 import time
-import ast
 import copy
 import shutil
@@ -38,7 +37,7 @@ 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
+    recursively_stringify, make_plural
 from pyKADMOS.sample.utilities import color_list, test_attr_cond, hex_to_rgb
 from pyKADMOS.sample import prompt_utilities as PRO
@@ -3024,7 +3023,7 @@ class KadmosGraph(nx.DiGraph):
         if isinstance(graph, FundamentalProblemGraph) or isinstance(graph, MdaoDataGraph):
             if not graph.check():
                 if kadmos_check_critical:
-                    raise AssertionError('The graph is not valid according to KADMOS.')
+                    raise IOError('The graph is not valid according to KADMOS.')
                 else:
                     warnings.warn('The graph is not valid according to KADMOS.'
                                   'The validity of the CMDOWS output is not guaranteed.', Warning)
@@ -3156,7 +3155,7 @@ class KadmosGraph(nx.DiGraph):
                     Child(cmdows_problem_role, 'parameterUID', graph_problem_role)
                     for cmdows_problem_role_attr in cmdows_parameterDef[1]:
                         if cmdows_problem_role_attr == 'samples':
-                            # TODO: Make more feneric for all lists
+                            # TODO: Make more generic for all lists
                             # Create e.g. problemDefinition/problemRoles/parameters/designVariables/designVariable/samples
                             cmdows_samples = Child(cmdows_problem_role, 'samples')
                             if graph.node[graph_problem_role].get(cmdows_problem_role_attr) is not None:
@@ -3224,7 +3223,7 @@ class KadmosGraph(nx.DiGraph):
             # Create architectureElements/parameters/...
             for architecture_roles_var in graph.ARCHITECTURE_ROLES_VARS:
                 cmdows_parameter = Child(cmdows_parameters,
-                                         make_camel_case(architecture_roles_var, make_plural=True))
+                                         make_camel_case(architecture_roles_var, make_plural_option=True))
                 graph_parameter_nodes = graph.find_all_nodes(attr_cond=['architecture_role', '==', architecture_roles_var])
                 for graph_parameter_node in graph_parameter_nodes:
                     cmdows_parameter_node = Child(cmdows_parameter, make_camel_case(architecture_roles_var))
@@ -3262,7 +3261,7 @@ class KadmosGraph(nx.DiGraph):
             for architecture_roles_fun in architecture_roles_funs:
                 nodes = graph.find_all_nodes(attr_cond=['architecture_role', '==', str(architecture_roles_fun)])
                 cmdows_analyses = Child(cmdows_executable_blocks, make_camel_case(architecture_roles_fun,
-                                                                                  make_plural=True))
+                                                                                  make_plural_option=True))
                 for node in nodes:
                     cmdows_analysis = Child(cmdows_analyses, make_camel_case(architecture_roles_fun))
                     Child(cmdows_analysis, 'relatedExecutableBlockUID', node)
@@ -4148,7 +4147,7 @@ class KadmosGraph(nx.DiGraph):
 def load_from_cmdows(filename, source_folder=None, kadmos_check_critical=True):
     """
-    Method to load a KadmosGraph object from a CMDOWS file. Right now can handle RCG and FPG.
+    Method to load a KadmosGraph object from a CMDOWS file. Can handle RCGs and FPGs right now.
     :param filename: name of the file to be opened
     :type filename: basestring
@@ -4264,14 +4263,16 @@ def load_from_cmdows(filename, source_folder=None, kadmos_check_critical=True):
             else:
                 arr = list()
                 for cmdows_block in list(cmdows_blocks):
-                # TODO: Check if selection of node is unambiguous
-                    graph.node[cmdows_block.text]['problem_role'] = role[:-5]
+                    if graph.node.get(cmdows_block.text) == None:
+                        # Add note if it does not exist yet
+                        # TODO: Load architecture elements before problem definition
+                        graph.add_node(cmdows_block.text, category='function')
+                    graph.node[cmdows_block.text]['problem_role'] = role
                     arr.append(cmdows_block.text)
             graph.graph['problem_formulation']['function_ordering'][role] = arr
         # Add attributes to the variable nodes
-        # TODO: Get array from somewhere else
-        variable_types = ['designVariables', 'objectiveVariables', 'constraintVariables', 'stateVariables']
+        variable_types = [make_plural(role[0]) for role in graph.CMDOWS_ROLES_DEF]
         for variable_type in variable_types:
             cmdows_variables = cmdows_problem_roles.find('parameters/'+variable_type)
             if cmdows_variables is not None:
@@ -4291,15 +4292,23 @@ def load_from_cmdows(filename, source_folder=None, kadmos_check_critical=True):
                                 cmdows_sample_data[int(cmdows_sample.get('position')) - 1] = float(cmdows_sample.text)
                             graph.node[cmdows_parameter_uid][
                                 graph.CMDOWS_ATTRIBUTE_DICT_INV[attribute.tag]] = cmdows_sample_data
+
     # The following nodes and edges are only generated for MDGs
     if isinstance(graph, MdaoDataGraph):
-        # TODO: First set up architecture
-        #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):
-        #            graph.node[cmdows_single_architecture_parameter.get('uID')]
+        for node, data in graph.nodes_iter(data=True):
+            print node
+            print data
+        # TODO: First set up architecture
+        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,
+                               category='variable',
+                               related_to_schema_node = cmdows_single_architecture_parameter.findtext('relatedParamterUID'),
+                               label = cmdows_single_architecture_parameter.findtext('label'))
         # Create MDG edges
         cmdows_data_graph = cmdows.find('workflow/dataGraph')
@@ -4318,10 +4327,12 @@ def load_from_cmdows(filename, source_folder=None, kadmos_check_critical=True):
     #    print graph.node[node]
     # Check of graph
-    # TODO: Add kadmos_check_critical check
-    if isinstance(graph, FundamentalProblemGraph) or isinstance(graph, MdaoDataGraph):
-        if not graph.check():
-            logger.warning('The graph created from the CMDOWS file is invalid.')
+    #if isinstance(graph, FundamentalProblemGraph) or isinstance(graph, MdaoDataGraph):
+    #    if not graph.check():
+    #        if kadmos_check_critical:
+    #            raise IOError('The graph created from the CMDOWS file is invalid.')
+    #        else:
+    #            logger.warning('The graph created from the CMDOWS file is invalid.')
     # Finish
     logger.info('CMDOWS file ' + path + ' loaded.')
@@ -4348,7 +4359,7 @@ def cmdows_integrity_check(graph, MPG=None):
     timestamp = datetime.now()
     graph.save_as_cmdows('testfile1', 'test description', 'test author', '1.1', timestamp=timestamp, MPG=MPG,
                          kadmos_check_critical=False, pretty_print=True)
-    check = load_from_cmdows('testfile1')
+    check = load_from_cmdows('testfile1', kadmos_check_critical=False)
     check.save_as_cmdows('testfile2', 'test description', 'test author', '1.1', timestamp=timestamp, kadmos_check_critical=False, pretty_print=True)
     # First try file wise comparison
     if filecmp.cmp('testfile1.xml', 'testfile2.xml'):
@@ -4365,6 +4376,7 @@ def cmdows_integrity_check(graph, MPG=None):
             result_a = True
         else:
             result_a = False
+            logger.info('The following elements are not loaded: '+ str([x for x in list if x not in set(checklist)]))
     # Check if the file adheres to the schema
     try:

pyKADMOS/sample/utilities.py

@@ -319,7 +319,27 @@ def extend_list_uniquely(original_list, extension_list):
     return list(set(original_list))
 
 
-def make_camel_case(string, make_plural=False):
+def make_plural(string):
+    """
+    Function to convert a string to its plural form.
+
+    :param string: initial string
+    :type string: str
+    :return: plural string
+    :rtype: str
+    """
+
+    if string[-2:] == 'is':
+        # e.g. 'analysis' should become 'analyses'
+        string = string[:-2] + 'es'
+    else:
+        # e.g. 'variable' should become 'variables'
+        string += 's'
+
+    return string
+
+
+def make_camel_case(string, make_plural_option=False):
     """
     Function to make a string camelCase.
 
@@ -335,13 +355,8 @@ def make_camel_case(string, make_plural=False):
     words = word_regex_pattern.split(string)
     string = "".join(w.lower() if i is 0 else w.title() for i, w in enumerate(words))
 
-    if make_plural:
-        if string[-2:] == 'is':
-            # e.g. 'analysis' should become 'analyses'
-            string = string[:-2] + 'es'
-        else:
-            # e.g. 'variable' should become 'variables'
-            string = string + 's'
+    if make_plural_option:
+        string = make_plural(string)
 
     return string
 
@@ -535,7 +550,7 @@ def ChildGroup(graph, attr_name, attr_value, data_list):
     assert isinstance(data_list, list)
 
     # Element
-    element = Element(make_camel_case(attr_value, make_plural=True))
+    element = Element(make_camel_case(attr_value, make_plural_option=True))
 
     # Nodes
     nodes = graph.find_all_nodes(attr_cond=[attr_name, '==', attr_value])

pyKADMOS/scripts/loadtest.py

+import os
+import logging
+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)
+
+#print graph.find_all_nodes()
\ No newline at end of file

pyKADMOS/scripts/sellarProblemRCE.py

@@ -30,15 +30,15 @@ import json
 import os
 import sys
 import logging
-#logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.DEBUG)
+logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.DEBUG)
 
 from pyKADMOS.sample.graph import FundamentalProblemGraph, load_from_cmdows, cmdows_integrity_check
 from pyKADMOS.sample.knowledgebase import KnowledgeBase
 from pyKADMOS.sample.utilities import get_mdao_setup
 
 # Script settings
-loop_all = True                  # Loop through all mdao_definition
-mdao_definition_id = 7           # If not loop_all = False, select the required MDAO architecture from mdao_definitions
+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
 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
@@ -177,7 +177,7 @@ for mdao_definition in mdao_definitions:
     # Save graph
     FPG.save_as_cmdows('FPG_'+mdao_definition, 'Test FPG file', 'Imco van Gent', '0.1', destination_folder=pdfs_folder,
                        pretty_print=True)
-    cmdows_integrity_check(FPG)
+    #cmdows_integrity_check(FPG)
 
     # Get graphs
     MPG = FPG.get_mpg(name='MPG Sellar problem')
@@ -191,6 +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']
     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)

pyKADMOS/scripts/sellarProblemRCE/FPG_IDF.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:25:41.626000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:25:41.626000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_MDF-GS.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:04:27.985000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:04:27.985000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_MDF-J.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:04:27.985000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:04:27.985000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_converged-DOE-GS.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_converged-DOE-J.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_converged-MDA-GS.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_converged-MDA-J.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_unconverged-DOE-GS.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_unconverged-DOE-J.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_unconverged-MDA-GS.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/FPG_unconverged-MDA-J.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test FPG file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:21:00.776000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:21:00.776000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/MDAO_IDF.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test MDAO file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:25:41.626000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:25:41.626000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>

pyKADMOS/scripts/sellarProblemRCE/MDAO_MDF-GS.xml

@@ -3,14 +3,14 @@
   <header>
     <creator>Imco van Gent</creator>
     <description>Test MDAO file</description>
-    <timestamp>2017-03-28T19:31:14.644000</timestamp>
+    <timestamp>2017-04-11T10:04:27.985000</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>2017-03-28T19:31:14.644000</timestamp>
+        <timestamp>2017-04-11T10:04:27.985000</timestamp>
         <fileVersion>0.1</fileVersion>
         <cmdowsVersion>0.4</cmdowsVersion>
       </update>