Moved demos .py to notebooks. Note: Maybe turn them to jupyternotebooks for consistency

notebooks/demo_h5_file_2_obis_props_mapping.py

@@ -0,0 +1,66 @@
+import src.openbis_lib as openbis_lib
+import hdf5_lib
+import datetime
+import os
+import logging
+
+def main():
+
+    #df_h5 = hdf5_lib.read_hdf5_as_dataframe_v2('BeamTimeMetaData.h5')
+    #df_h5['lastModifiedDatestr'] = df_h5['lastModifiedDatestr'].astype('datetime64[ns]')
+    #df_h5 = df_h5.sort_values(by='lastModifiedDatestr')
+
+    
+    openbis_obj = openbis_lib.initialize_openbis_obj()
+    
+    # Create df with sample measurements of type 'ISS_MEASUREMENT'
+    samples = openbis_obj.get_samples(type='ISS_MEASUREMENT',props=['FILENUMBER'])
+    for sample in samples:
+        print(type(sample))
+        print(sample.identifier)
+    df_openbis = samples.df.copy(deep=True)
+    h5_file_path = os.path.join(os.path.curdir,'input_files\\BeamTimeMetaData.h5')
+    df_h5 = hdf5_lib.read_hdf5_as_dataframe(h5_file_path)
+
+    # dataframe preprocessing steps
+    df_h5, df_openbis = openbis_lib.align_datetime_observation_windows(df_h5, df_openbis)    
+    df_openbis = openbis_lib.pair_openbis_and_h5_dataframes(df_openbis, df_h5, 'REFORMATED_FILENUMBER', 'name')
+
+    
+
+    current_date = datetime.date.today()
+    log_filename = 'logs\\computed_openbis_props_logs_' + current_date.strftime('%d-%m-%Y') + '.log'
+    logging_flag = True
+
+    #logger = logging.getLogger(__name__)
+    #logger.setLevel(logging.DEBUG)
+
+    log_file_path = os.path.join(os.path.curdir,log_filename)
+
+    logging.basicConfig(filename=log_file_path,
+                        level=logging.DEBUG,
+                        format="%(asctime)s %(levelname)s %(message)s",                        
+                        datefmt="%d-%m-%Y %H:%M:%S",
+                        )  
+
+    for sample_idx in df_openbis.index:
+
+        #    logging.basicConfig(log_filename)
+        #print(formatted_dict)
+        sample_props_dict = openbis_lib.compute_openbis_sample_props_from_h5(df_openbis, df_h5, sample_idx)
+
+        formatted_dict = [f"{key}:{value}" for key, value in sample_props_dict.items()]
+        formatted_dict = "\n".join(formatted_dict)
+
+        logging.debug('\n'+formatted_dict)
+
+        
+        #print(props_dict)
+    openbis_obj.logout()
+
+    # Choose samples and specifici properties to update: create a log 
+
+
+if __name__=="__main__":
+    main()
+

notebooks/demo_single_sample_update_to_openbis.py

@@ -0,0 +1,88 @@
+import os, sys
+sys.path.append(os.path.abspath('src'))
+
+import src.openbis_lib as openbis_lib
+import src.hdf5_lib as hdf5_lib
+import datetime
+import os
+import logging
+
+def main():
+
+    #df_h5 = hdf5_lib.read_hdf5_as_dataframe_v2('BeamTimeMetaData.h5')
+    #df_h5['lastModifiedDatestr'] = df_h5['lastModifiedDatestr'].astype('datetime64[ns]')
+    #df_h5 = df_h5.sort_values(by='lastModifiedDatestr')
+
+    
+    openbis_obj = openbis_lib.initialize_openbis_obj()
+    
+    # Create df with sample measurements of type 'ISS_MEASUREMENT'
+    samples = openbis_obj.get_samples(type='ISS_MEASUREMENT',props=['FILENUMBER'])
+    for sample in samples:
+        print(type(sample))
+        print(sample.identifier)
+    df_openbis = samples.df.copy(deep=True)
+    h5_file_path = os.path.join(os.path.curdir,'input_files\\BeamTimeMetaData.h5')
+    df_h5 = hdf5_lib.read_mtable_as_dataframe(h5_file_path)
+
+    # dataframe preprocessing steps
+    df_h5, df_openbis = openbis_lib.align_datetime_observation_windows(df_h5, df_openbis)    
+    df_openbis = openbis_lib.pair_openbis_and_h5_dataframes(df_openbis, df_h5, 'REFORMATED_FILENUMBER', 'name')
+
+    
+
+    current_date = datetime.date.today()
+    log_filename = 'logs\\computed_openbis_props_logs_' + current_date.strftime('%d-%m-%Y') + '.log'
+    logging_flag = True
+
+    #logger = logging.getLogger(__name__)
+    #logger.setLevel(logging.DEBUG)
+
+    log_file_path = os.path.join(os.path.curdir,log_filename)
+
+    logging.basicConfig(filename=log_file_path,
+                        level=logging.DEBUG,
+                        format="%(asctime)s %(levelname)s %(message)s",                        
+                        datefmt="%d-%m-%Y %H:%M:%S",
+                        )  
+
+    # update sample properties in openbis database only if they are labeled as bad
+
+    props_include_list = ['sample_name', 'temp', 'cell_pressure','method_name', 'region', 'lens_mode', 'acq_mode', 'dwell_time']
+    props_include_list = ['ke_range_center','ke_range_step']
+    props_include_list = [ 'temp', 'cell_pressure','photon_energy','dwell_time','passenergy','ke_range_center','ke_step_center','position_x','position_y','position_z']
+    
+    props_include_list = ['position_x','position_y','position_z']
+    props_include_list = [ 'temp', 'cell_pressure','photon_energy','dwell_time','passenergy','ke_range_center','ke_step_center']
+
+
+    for sample_idx in df_openbis.index:
+
+        #    logging.basicConfig(log_filename)
+        #print(formatted_dict)
+        sample_props_dict = openbis_lib.compute_openbis_sample_props_from_h5(df_openbis, df_h5, sample_idx)
+
+        #sample_props_dict[ke_range_center]
+
+        formatted_dict = [f"{key}:{value}" for key, value in sample_props_dict.items()]
+        formatted_dict = "\n".join(formatted_dict)
+        logging.debug('\n'+formatted_dict)
+        try:
+            filenumber = -1 if sample_props_dict['FILENUMBER'] == '' else int(sample_props_dict['FILENUMBER'])
+            
+            if filenumber >= 85 :
+                print(filenumber)
+            #if 'bad' in sample_props_dict['sample_name']:
+                logging.info('The above sample is to be updated in openbis:')                
+                openbis_lib.single_sample_update(sample_props_dict,samples,props_include_list)
+        except KeyError:
+            logging.error(KeyError)
+        #print(props_dict)
+    openbis_obj.logout()
+
+    # Choose samples and specifici properties to update: create a log 
+
+
+if __name__=="__main__":
+    main()
+