Merge branch 'master' of https://github.com/BSC-ES/providentia

Author: PaulaSerranoSierra

providentia/configuration.py

@@ -1116,6 +1116,14 @@ def check_validity(self, deactivate_warning=False):
             show_message(self.read_instance, msg, from_conf=self.read_instance.from_conf, deactivate=deactivate_warning)
             self.read_instance.species = default
 
+        # chech resolution
+        # if not interpolation or download, get first resolution in list
+        if (',' in self.read_instance.resolution) and (self.read_instance.mode not in ['interpolation', 'download']):
+            default = self.read_instance.resolution.split(',')[0]
+            msg = "Resolution (resolution) contains multiple values. Using '{}' as default.".format(default)
+            show_message(self.read_instance, msg, from_conf=self.read_instance.from_conf, deactivate=deactivate_warning)
+            self.read_instance.resolution = default
+            
         # if number of networks and species is not the same,
         # and len of one of network or species == 1,
         # then duplicate respestive network/species

providentia/read_aux.py

@@ -963,7 +963,7 @@ def valid_date(date_text):
         return False
 
 
-def generate_file_trees(instance, force=False):
+def generate_file_trees(instance):
     """ Generate file trees. Force if we want to remove depedency on the machine.
     """
 
@@ -982,29 +982,45 @@ def generate_file_trees(instance, force=False):
         gft = True
 
     # generate file trees
-    if gft or force:
-        instance.logger.info('Generating file trees...')
-        instance.all_observation_data = get_ghost_observational_tree(instance)
-        if instance.nonghost_root is not None:
-            nonghost_observation_data = get_nonghost_observational_tree(instance)
+    ghost_filetree_path = join(PROVIDENTIA_ROOT, 'settings/internal/ghost_filetree_{}.json'.format(instance.ghost_version)) 
+    nonghost_filetree_path = join(PROVIDENTIA_ROOT, 'settings/internal/nonghost_filetree.json') 
+
+    # generate file trees for ghost
+    if gft or (not os.path.exists(ghost_filetree_path)):
+        if not os.path.exists(ghost_filetree_path):
+            instance.logger.info(f'Generating file tree {ghost_filetree_path}...')
+        else:
+            instance.logger.info(f'Updating file tree {ghost_filetree_path}...')
+        instance.all_observation_data = get_ghost_observational_tree(instance) 
     # load file trees
     else:
+        instance.logger.info(f'Loading file tree {ghost_filetree_path}...')
         try:
             instance.all_observation_data = json.load(open(join(PROVIDENTIA_ROOT, 'settings/internal/ghost_filetree_{}.json'.format(instance.ghost_version)))) 
         except FileNotFoundError as file_error:
             error = "Error: Trying to load 'settings/internal/ghost_filetree_{}.json' but file does not exist. Run with the flag '--gft' to generate this file.".format(instance.ghost_version)
             instance.logger.error(error)
             sys.exit(1)
-        if instance.nonghost_root is not None:
+
+    if instance.nonghost_root is not None:
+        # generate file trees for nonghost
+        if gft or (not os.path.exists(nonghost_filetree_path)):
+            if not os.path.exists(nonghost_filetree_path):
+                instance.logger.info(f'Generating file tree {nonghost_filetree_path}...')
+            else:
+                instance.logger.info(f'Updating file tree {nonghost_filetree_path}...')
+            nonghost_observation_data = get_nonghost_observational_tree(instance)
+        # load file trees
+        else:
+            instance.logger.info(f'Loading file tree {nonghost_filetree_path}...')
             try:
                 nonghost_observation_data = json.load(open(join(PROVIDENTIA_ROOT, 'settings/internal/nonghost_filetree.json')))
             except FileNotFoundError as file_error:
                 error = "Error: Trying to load 'settings/internal/nonghost_filetree.json' but file does not exist. Run with the flag '--gft' to generate this file."
                 instance.logger.error(error)
                 sys.exit(1)
 
-    # merge GHOST and non-GHOST filetrees
-    if instance.nonghost_root is not None:
+        # merge GHOST and non-GHOST filetrees
         instance.all_observation_data = {**instance.all_observation_data, **nonghost_observation_data}
 
 

providentia/report.py

@@ -149,12 +149,7 @@ def __init__(self, **kwargs):
 
             # if first section or GHOST version has changed
             if (section_ind == 0) or (current_ghost_version != self.ghost_version):
-                # if GHOST version has changed, generate file trees always (independently of the machine)
-                if (current_ghost_version != self.ghost_version):
-                    generate_file_trees(self, force=True)
-                # if it hasn't and we are in the first section, generate if needed
-                else:
-                    generate_file_trees(self)
+                generate_file_trees(self)
 
                 # initialise DataReader class
                 self.datareader = DataReader(self)

providentia/toolbar.py

@@ -396,7 +396,7 @@ def reload_conf(self, section, fpath):
 
         # generate file trees if GHOST version has changed
         if current_ghost_version != self.read_instance.ghost_version:
-            generate_file_trees(self.read_instance, force=True)
+            generate_file_trees(self.read_instance)
 
         # update species, experiments, qa & flags
         self.read_instance.config_bar_initialisation = True