Added warnings on missing optional things, and a flag to ignore the w…

…arnings

checksit/check.py

@@ -20,13 +20,14 @@
 class Checker:
 
     def __init__(self, template="auto", mappings=None, extra_rules=None, specs=None, ignore_attrs=None, 
-                auto_cache=False, verbose=False, log_mode="standard"):
+                auto_cache=False, verbose=False, log_mode="standard", ignore_warnings=False):
         self.template = template
         self.mappings = mappings or {}
         self.extra_rules = extra_rules or {}
         self.specs = specs or []
         self.ignore_attrs = ignore_attrs or []
         self.auto_cache = auto_cache
+        self.ignore_warnings = ignore_warnings
         self.verbose = verbose
         self.log_mode = log_mode
         self._check_context = {}
@@ -123,7 +124,7 @@ def _compare_dicts(self, record, template, label, mappings=None, ignore_attrs=No
         return errors
 
     def _check_file(self, file_content, template, mappings=None, extra_rules=None, specs=None,
-                        ignore_attrs=None, log_mode="standard", fmt_errors=None):
+                        ignore_attrs=None, log_mode="standard", fmt_errors=None, ignore_warnings=False):
 
         if hasattr(file_content, "to_dict"):
             record = file_content.to_dict()
@@ -136,13 +137,16 @@ def _check_file(self, file_content, template, mappings=None, extra_rules=None, s
 
         # Create a container for collecting errors
         errors = getattr(file_content, "fmt_errors", [])
+        warnings = []
 
         # Use check specifications if requested
         specs = specs or self.specs
 
         for spec in specs:
             sr = SpecificationChecker(spec)
-            errors.extend(sr.run_checks(record))
+            spec_errors, spec_warnings = sr.run_checks(record)
+            errors.extend(spec_errors)
+            warnings.extend(spec_warnings)
 
         if template == "off" and log_mode == "standard":
             print("[WARNING] Template checks switched off!")
@@ -166,11 +170,22 @@ def _check_file(self, file_content, template, mappings=None, extra_rules=None, s
                 for i, error in enumerate(errors):
                     count = i + 1
                     print(f"\t{count:02d}. {error}")
+                compliant = False
             else:
+                compliant = True
+
+            if warnings and not ignore_warnings:
+                print(f"\n[WARNING] {len(warnings)} warnings about file:\n")
+                for i, warning in enumerate(warnings):
+                    count = i + 1
+                    print(f"\t{count:02d}. {warning}")
+
+            if compliant:
                 print("[INFO] File is compliant!")            
 
+
     def check_file(self, file_path, template="auto", mappings=None, extra_rules=None, specs=None,
-                ignore_attrs=None, auto_cache=False, verbose=False, log_mode="standard"):
+                ignore_attrs=None, auto_cache=False, verbose=False, log_mode="standard", ignore_warnings=False):
 
         try:
             fp = FileParser()
@@ -234,7 +249,7 @@ def check_file(self, file_path, template="auto", mappings=None, extra_rules=None
             print(f"\nRunning with:\n\tTemplate: {tmpl_input}\n\tSpec Files: {specs}\n\tDatafile: {file_content.inpt}")
 
         self._check_file(file_content, template=tmpl, mappings=mappings, extra_rules=extra_rules, 
-                        specs=specs, ignore_attrs=ignore_attrs, log_mode=log_mode)
+                        specs=specs, ignore_attrs=ignore_attrs, log_mode=log_mode, ignore_warnings=ignore_warnings)
 
 
 class TemplateManager:

checksit/cli.py

@@ -33,9 +33,10 @@ def main():
 @click.option("-l", "--log-mode", default="standard")
 @click.option("-v", "--verbose/--no-verbose", default=False)
 @click.option("-t", "--template", default="auto")
+@click.option("-w", "--ignore-warnings", is_flag=True)
 def check(file_path, mappings=None, rules=None, specs=None, ignore_attrs=None, ignore_all_globals=False,
           ignore_all_dimensions=False, ignore_all_variables=False, ignore_all_variable_attrs=False,
-          auto_cache=False, log_mode="standard", verbose=False, template="auto"):
+          auto_cache=False, log_mode="standard", verbose=False, template="auto", ignore_warnings=False):
 
     if ignore_all_globals or ignore_all_dimensions or ignore_all_variables or ignore_all_variable_attrs:
         raise Exception("Options not implemented yet!!!!!")
@@ -55,7 +56,7 @@ def check(file_path, mappings=None, rules=None, specs=None, ignore_attrs=None, i
     return check_file(file_path, template=template, mappings=mappings, extra_rules=rules, 
                 specs=specs, ignore_attrs=ignore_attrs, 
                 auto_cache=auto_cache, verbose=verbose, 
-                log_mode=log_mode)
+                log_mode=log_mode, ignore_warnings=ignore_warnings)
 
 
 @main.command()

checksit/generic.py

@@ -17,6 +17,8 @@ def check_var_attrs(dct, defined_attrs, ignore_bounds=True):
     E.g.: check-var-attrs:defined_attrs:long_name|units
     """
     errors = []
+    warnings = []
+
     bounds_vars = _get_bounds_var_ids(dct)
 
     for var_id, var_dict in dct["variables"].items():
@@ -26,7 +28,7 @@ def check_var_attrs(dct, defined_attrs, ignore_bounds=True):
             if is_undefined(var_dict.get(attr)):
                 errors.append(f"[variable**************:{var_id}]: Attribute '{attr}' must have a valid definition.")
 
-    return errors
+    return errors, warnings
 
 
 def check_global_attrs(dct, defined_attrs=None, vocab_attrs=None, regex_attrs=None, rules_attrs=None):
@@ -42,6 +44,7 @@ def check_global_attrs(dct, defined_attrs=None, vocab_attrs=None, regex_attrs=No
     rules_attrs = rules_attrs or {}
 
     errors = []
+    warnings = []
 
     for attr in defined_attrs:
         if is_undefined(dct['global_attributes'].get(attr)):
@@ -58,7 +61,7 @@ def check_global_attrs(dct, defined_attrs=None, vocab_attrs=None, regex_attrs=No
         errors.extend(rules.check(rules_attrs[attr], dct['global_attributes'].get(attr, UNDEFINED), label=f"[global-attributes:******:{attr}]***"))
 
 
-    return errors
+    return errors, warnings
 
 
 def check_var_exists(dct, variables):
@@ -68,18 +71,18 @@ def check_var_exists(dct, variables):
     E.g. check-var-exists:variables:time|altitude
     """
     errors = []
+    warnings = []
 
     for var in variables:
         if ':__OPTIONAL__' in var:
             var = var.split(':')[0]
             if var not in dct["variables"].keys():
-                # add warning/advisory
-                pass
+                warnings.append(f"[variable**************:{var}]: Optional variable does not exist in file.")
         else:
             if var not in dct["variables"].keys():
                 errors.append(f"[variable**************:{var}]: Does not exist in file.")
 
-    return errors
+    return errors, warnings
 
 
 def check_dim_exists(dct, dimensions):
@@ -89,31 +92,32 @@ def check_dim_exists(dct, dimensions):
     E.g. check-dim-exists:dimensions:time|latitude
     """
     errors = []
+    warnings = []
 
     for dim in dimensions:
         if ':__OPTIONAL__' in dim:
             dim = dim.split(':')[0]
             if dim not in dct["dimensions"].keys():
-                # add warning/advisory
-                pass
+                warnings.append(f"[dimension**************:{dim}]: Optional dimension does not exist in file.")
         else:
             if dim not in dct["dimensions"].keys():
                 errors.append(f"[dimension**************:{dim}]: Does not exist in file.")
 
-    return errors 
+    return errors, warnings 
 
 
 def check_var(dct, variables, defined_attrs):
     """
     Check variables exist and have attributes defined.
     """
     errors = []
+    warnings = []
+
     for var in variables:
         if ':__OPTIONAL__' in var:
             var = var.split(':')[0]
             if var not in dct["variables"].keys():
-                # add warning/advisory
-                pass
+                warnings.append(f"[variable**************:{var}]: Optional variable does not exist in file.")
             else:
                 for attr in defined_attrs:
                     if is_undefined(dct["variables"][var].get(attr)):
@@ -126,4 +130,4 @@ def check_var(dct, variables, defined_attrs):
                     if is_undefined(dct["variables"][var].get(attr)):
                         errors.append(f"[variable**************:{var}]: Attribute '{attr}' must have a valid definition.")            
 
-    return errors
+    return errors, warnings

checksit/specs.py

@@ -60,8 +60,11 @@ def _run_check(self, record, check_dict):
 
     def run_checks(self, record):
         errors = []
+        warnings = []
 
         for check_id, check_dict in self.spec.items():
-            errors.extend(self._run_check(record, check_dict)) 
+            check_errors, check_warnings = self._run_check(record, check_dict)
+            errors.extend(check_errors)
+            warnings.extend(check_warnings) 
 
-        return errors
+        return errors, warnings