diff --git a/demo_single_sample_update_to_openbis.py b/demo_single_sample_update_to_openbis.py index 7cc3830..e77eae9 100644 --- a/demo_single_sample_update_to_openbis.py +++ b/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) diff --git a/environment.yml b/environment.yml index c9009cc..75056c1 100644 --- a/environment.yml +++ b/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 diff --git a/input_files/config_file.py b/input_files/config_file.py index 0497e83..bc88215 100644 --- a/input_files/config_file.py +++ b/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 = 'unified_file_smog_chamber_2024-03-19_UTC-OFST_+0100_NG.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' ext_to_reader_dict = {'.txt': scf_reader.read_txt_files_as_dict,