Allow !include tag in ontology yaml

-- yaml loader added a constructor function in helpers.py to allow !inlcude tag
	- !include <yaml filename> will then input the contents of that file into the main yaml when reading it in
-- small update to project.addMooring() to allow input of a subsystem in lieu of a design dictionary
-- small bug fix in project.addMooring()

Author: lsirkis

famodel/helpers.py

@@ -67,7 +67,64 @@ def unitVector(r):
     return r/L
 
 
+def loadYAML(filename):
+    '''
+    Loads a YAML file, allowing !include <filename> to include another yaml 
+    in the file.
+
+    Parameters
+    ----------
+    filename : str
+        Filename (including path if needed) of main yaml file to load
+
+    Returns
+    -------
+    info : dict
+        Dictionary loaded from yaml
+
+    '''
+    
+    with open(filename) as file:
+        loader = yaml.FullLoader 
+        loader.add_constructor('!include',yamlInclude)
+        project = yaml.load(file, Loader=loader)
+        if not project:
+            raise Exception(f'File {file} does not exist or cannot be read. Please check filename.')
+    
+    return(project)
 
+def yamlInclude(loader, node):
+    '''
+    Custom constructor that allows !include tag to include another yaml in
+    the main yaml
+
+    Parameters
+    ----------
+    loader : YAML loader object
+    node : YAML node
+        YAML node for include
+
+    Returns
+    -------
+    None.
+
+    '''
+    # pull out f
+    file_to_include = loader.construct_scalar(node)
+    # pull out absolute path of file
+    # if os.path.isabs(file_to_include):
+    #     included_yaml = file_to_include
+    # else:
+    #     dir = 
+    included_yaml = os.path.abspath(file_to_include)
+    try:
+        with open(included_yaml) as file:
+            return(yaml.load(file,Loader=loader.__class__))
+    except FileNotFoundError:
+        raise FileNotFoundError(f"Included file {included_yaml} not found")
+    except Exception as err:
+        raise Exception(f"Error ocurred while loading included file {included_yaml}: {err}")
+    
 
 # ----- Cable routing support functions -----
 

famodel/project.py

@@ -34,7 +34,7 @@
 # Import select required helper functions
 from famodel.helpers import (check_headings, head_adjust, getCableDD, getDynamicCables, 
                             getMoorings, getAnchors, getFromDict, cleanDataTypes, 
-                            getStaticCables, getCableDesign,m2nm)
+                            getStaticCables, getCableDesign,m2nm, loadYAML)
 
 
 class Project():
@@ -129,7 +129,7 @@ def __init__(self, lon=0, lat=0, file=None, depth=202,raft=1):
 
 
 
-    def load(self, info,raft=1):
+    def load(self, info, raft=True):
         '''
         Load a full set of project information from a dictionary or 
         YAML file. This calls other methods for each part of it.
@@ -141,10 +141,12 @@ def load(self, info,raft=1):
         '''
         # standard function to load dict if input is yaml
         if isinstance(info,str):
-            with open(info) as file:
-                project = yaml.load(file, Loader=yaml.FullLoader)
-                if not project:
-                    raise Exception(f'File {file} does not exist or cannot be read. Please check filename.')
+            
+            # with open(info) as file:
+            #     project = yaml.load(file, Loader=yaml.FullLoader)
+            #     if not project:
+            #         raise Exception(f'File {file} does not exist or cannot be read. Please check filename.')
+            project = loadYAML(info)
         else:
             project = info
 
@@ -161,7 +163,7 @@ def load(self, info,raft=1):
 
     # ----- Design loading/processing methods -----
 
-    def loadDesign(self, d, raft=1):
+    def loadDesign(self, d, raft=True):
         '''Load design information from a dictionary or YAML file
         (specified by input). This should be the design portion of
         the floating wind array ontology.'''
@@ -1485,7 +1487,8 @@ def addPlatform(self,r=[0,0,0], id=None, phi=0, entity='',
     def addMooring(self, id=None, endA=None, endB=None, heading=0, dd={}, 
                    section_types=[], section_lengths=[], 
                    connectors=[], span=0, shared=0, reposition=False, adjuster=None,
-                   method = 'horizontal', target = None, i_line = 0):
+                   method = 'horizontal', target = None, i_line = 0, subsystem=None):
+
         '''
         Function to create a mooring object  and save in mooringList
         Optionally does the following:
@@ -1552,7 +1555,7 @@ def addMooring(self, id=None, endA=None, endB=None, heading=0, dd={},
             else:
                 id = 'moor'+str(len(self.mooringList))
 
-        if not dd:
+        if not dd and len(section_types) > 0:
             sections = [{'type':section_types[i],'L':section_lengths[i]} for i in range(len(section_types))]
             if len(connectors) == 0 and len(sections) != 0:
                 connectors = [{}]*len(sections)+1
@@ -1563,21 +1566,23 @@ def addMooring(self, id=None, endA=None, endB=None, heading=0, dd={},
                   'rad_fair':self.platformList[id_part[0]].rFair if id_part else 0,
                   'z_fair':self.platformList[id_part[0]].zFair if id_part else 0}
 
-        mooring = Mooring(dd=dd, id=id) # create mooring object
+        mooring = Mooring(dd=dd, id=id, subsystem=subsystem) # create mooring object
 
         #calculate target pretension or horizontal tension if none provided
         if adjuster != None and target == None:
-            targetdd = deepcopy(dd)
+            targetdd = deepcopy(mooring.dd)
             targetdd['zAnchor'] = self.depth
-            mooring.createSubsystem(dd)
+            mooring.createSubsystem()
 
             if method == 'horizontal':
                 mooring.target = np.linalg.norm(mooring.ss.fB_L[:2])
             elif method =='pretension':
                 mooring.target = np.linalg.norm(mooring.ss.fB_L)
             else:
                 raise Exception('Invalid adjustment method. Must be pretension or horizontal')
-        
+        else:
+            mooring.target = target
+
         # update shared prop if needed
         if len(id_part)==2 and shared<1:
             shared = 1