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demo_single_sample_update_to_openbis.py

@@ -1,5 +1,8 @@
+import os, sys
+sys.path.append(os.path.abspath('src'))
+
 import src.openbis_lib as openbis_lib
-import hdf5_lib
+import src.hdf5_lib as hdf5_lib
 import datetime
 import os
 import logging
@@ -20,7 +23,7 @@ def main():
         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)
+    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)    

environment.yml

@@ -11,3 +11,9 @@ dependencies:
   - plotly=5.18
   - h5py=3.10
   - pybis=1.35
+  - openssl
+  - scipy
+# I installed openpyxl through anaconda manager from their default curated channels
+  - openpyxl=3.0.10
+  - pip:
+    - pygit2==1.14

input_files/config_file.py

@@ -1,9 +1,14 @@
+import sys
+import os
+root_dir = os.path.abspath(os.curdir)
+sys.path.append(root_dir)
+
 
 import src.smog_chamber_file_reader as scf_reader
 import src.g5505_file_reader as g5505f_reader
 from datetime import datetime
 import pandas as pd
-import os
+
 
 group_id = 'smog_chamber'
 
@@ -34,8 +39,8 @@ if group_id == 'smog_chamber':
 
     outputfile_dir = 'output_files'
 
-    #output_filename = output_filename_tempate(group_id,created_at,user_initials) #'test_smog_chamber_v14.h5'
+    output_filename = output_filename_tempate(group_id,created_at,user_initials) #'test_smog_chamber_v14.h5'
-    output_filename = 'unified_file_smog_chamber_2024-03-19_UTC-OFST_+0100_NG.h5'
+    #output_filename = 'unified_file_smog_chamber_2024-03-19_UTC-OFST_+0100_NG.h5'
 
 
     ext_to_reader_dict = {'.txt': scf_reader.read_txt_files_as_dict,