function for file export - success!

ArgoCanada · Mar 13, 2024 · 7f6af3a · 7f6af3a
1 parent 60d8579
commit 7f6af3a
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Showing 2 changed files with 48 additions and 6 deletions.
diff --git a/bgcArgoDMQC/core/prof.py b/bgcArgoDMQC/core/prof.py
@@ -29,8 +29,9 @@ class prof:
     def __init__(self, wmo, cycle, kind='C', keep_fillvalue=False, rcheck=True, verbose=False):
 
         self.__floatdict__, self.__prof__, self.__fillvalue__ = load_profile(io.Path.ARGO_PATH, wmo, cycle, kind=kind)
-        self.__rawfloatdict__ = self.__floatdict__
+        self.__rawfloatdict__ = copy.deepcopy(self.__floatdict__)
         self._dict = 'raw'
+        self._changelog = []
 
         # local path info
         self.argo_path = io.Path.ARGO_PATH
@@ -83,7 +84,7 @@ def reset(self):
         Reset all variables back to original loaded variables. Undoes the effect of
         clean(), rm_fillvalue(), check_range().
         '''
-        self.__floatdict__ = copy.deepcopy(self.__rawfloatdict__)
+        self.__floatdict__ = self.__rawfloatdict__
         self._dict = 'raw'
         self.to_dataframe()
 
@@ -166,12 +167,14 @@ def update_field(self, field, value, where=None):
         self.__floatdict__[field][where] = value
 
         self.set_dict(current_float_dict)
+        self._changelog.append(field)
         self.to_dataframe()
 
     def set_fillvalue(self, field, where=None):
 
         self.update_field(field, self.__fillvalue__[field], where)
 
-    def export_files(self):
+    def update_file(self, history):
 
-        io.update_nc(self.__floatdict__, self.__prof__)
+        export_file = io.update_nc(self.__floatdict__, self.__prof__, self._changelog, history_dict=history)
+        return export_file
diff --git a/bgcArgoDMQC/io/netcdf.py b/bgcArgoDMQC/io/netcdf.py
@@ -355,6 +355,45 @@ def export_delayed_files(fdict, files, gain, data_mode='D', comment=None, equati
         sys.stdout.write('done\n')
         D_nc.close()
 
-def update_nc(fdict, file, changelog, history_dict={}):
+def update_nc(fdict, fn, changelog, history_dict={}):
+
+    # get DATE_UPDATE
+    date_update = pd.Timestamp.now(tz='utc').strftime('%Y%m%d%H%M%S')
+
+    dac = fn.as_posix().split('/')[-4]
+    output_file = Path(fn.as_posix().replace(f'dac/{dac}/', f'dac/{dac}/E/'))
+    if not output_file.parent.exists():
+        output_file.parent.mkdir(parents=True)
+    sys.stdout.write(f'Working on file {output_file.as_posix()}...')
+
+    O_nc = copy_netcdf(fn, output_file)
+    if not O_nc.dimensions['N_HISTORY'].isunlimited():
+        O_nc.close()
+        O_nc = unlimit_dimension(fn, output_file, 'N_HISTORY')
+
+    for f in changelog:
+
+        O_nc[f][:] = fdict[f]
+
+        # if a changed value is QC flags, recalculate PROFILE_<PARAM>_QC
+        if f.split('_')[1] == 'QC':
+            for i in range(O_nc.dimensions['N_PROF'].size):
+                flags = read_qc(O_nc[f][:].data[i,:])
+                grade = profile_qc(pd.Series(flags)).encode('utf-8')
+                O_nc[f'PROFILE_{f}'][i] = grade
+
+    history = dict(
+        HISTORY_INSTITUTION=history_dict['HISTORY_INSTITUTION'],
+        HISTORY_STEP=history_dict['HISTORY_STEP'],
+        HISTORY_SOFTWARE='BGQC',
+        HISTORY_SOFTWARE_RELEASE='v0.2',
+        HISTORY_DATE=date_update,
+        HISTORY_ACTION=history_dict['HISTORY_ACTION']
+    )
 
-    return
+    O_nc['DATE_UPDATE'][:] = string_to_array(date_update, O_nc.dimensions['DATE_TIME'])
+    update_history(O_nc, history)
+    sys.stdout.write('done\n')
+    O_nc.close()
+
+    return output_file