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Created with Raphaël 2.2.014Mar1125Feb2422108764327Jan242221144Dec3226Nov2524232110129Oct281714109732130Sep2726251917161323Aug22161412987217Jul11109852121Jun2019181716131110743231May3029282726242322930Apr2625242318177543228Mar2726252221191821Feb161514132131Jan22Dec9Nov3231Oct262019181022AugFix import statement in pipelines.data_integration.pymainmainWIP: Update contributing and acknowledgement sections.Implemented hdf5_file_reader.py and updated register.yaml and hdf5_writer.py. This replaces previous function __copy_file_in_group().Merge branch 'feature/DB_for_FileReader_Repo' into 'main'Merge branch 'main' into 'feature/DB_for_FileReader_Repo'Update import statements in pipelines/data_integration.py. from instruments.readers import ... -> from instruments import ...Implemented create_hdf5_from_filesystem_new() using new instrument readers cml interface and subprocesses. This facilitates extension of file reading capabilities by collaborators without requiring changes to file_registry.py. Only additions in folders and registry.yaml.Update all file readers with command line interface so we can run them as a subprocess. Added also registry.yaml to decouple code from user-based instrument adaptations or extensions.Merge branch 'main' of https://gitlab.psi.ch/5505-public/dimaFix import for filereader_registry.py after moving it from intruments/readers/ one level above.Moved filereader_registry.py outside readers folder.Moved filereader_registry.py outside readers folder.Change import statements with try except to enable explicit import of submodules from import to avoid conflicts with parent project.Implement data_lineage_metadata.json detection and then use it to annotate associated file.Enable boolean type columns from pandas DataFrame to be suitably converted into numpy structured arrayMake file reader selection case insensitive by using ext.lower() and update config_text_reader.py to point to renamed dictionary.remove instruments/dictionaries/ICAD_NO2.yaml. Its dict terms are now in ICAD.yaml.Add dict terms from ICAD_NO2.yamlCombine dictionaries of ICAD_HONO.yaml and ICAD_NO2.yaml into ICAD.yamlRemove skip directory condition when directory keywords are empty. Here, all paths to files should be considered.Fix reader txt/csv default behavior.Enable instrumentFolder of form <instFolder>/<category>/ to be trasfered without flatenningAdd try except block to trigger errors for invalid group names.Add constraint to match only path/to/keyword1/keyword2/files containing a composite keyword keyword1/keyword2.Add property to extracted dataset as dataframe. Now time column is of datetime type to facilitate downstream procesing.Implement method in hdf5 manager to infer datetime column in datasetSynch with remote repoFix typo in html text.Update readme.md and set_up_env.shUpdate unload operation to remove reference and fix logic error to dataset metadata extraction.Add validation step to yaml file validation to ensure list type and a minimun length for the 'instrument_datafolder' keyword.Fix typo on extension items, extensions need to include a dot .json and .yaml.Add json and yaml extensions to admissible file extension lists.Updated to cleared jupyter notebooksAdded comments to explain configuration parameters/or variables.Add directory tree structure description.Update .gitignore with output_files/Add .gitkeep and keep this folder empty. it is only to be used for local processingUpdate readme with getting started sectionSolved binary incompatibility issue of generated environment by conda installing h5py and numpy from conda-forge or default channels.