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2dbd255589
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Created file reader for acsm tofware files, updated registry and updated yaml file with instrument specific terms and reader config params.
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2024-10-07 16:18:14 +02:00 |
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bd4ced00ba
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Fixed bug, causing input_path normalization operation to damage Windows network drive paths. Basically, os.path.normpath(path_to_input_directory).strip(os.sep) replaced by os.path.normpath(path_to_input_directory).rstrip(os.sep)
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2024-10-07 16:16:12 +02:00 |
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c103268102
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Fixed bugs in update_file() method and create_hdf5_file_from_filesystem_path()
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2024-10-03 09:32:25 +02:00 |
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2920be624a
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Added new instrument (flagging app) file reading capabilities. It includes two files a flag_reader.py that takes flag.json files produced by the app into a standard intermidiate representation, and a yaml file with instrument dependent description terms. Last, we modified the filereader_registry.py to find the new instrument file reader.
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2024-10-03 09:07:06 +02:00 |
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bac6f5d773
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Added __init__.py inside intrument folders
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2024-10-02 15:51:02 +02:00 |
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d49f511dbd
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Added .update_file() method, which enables complementary data structure updates to existing file with same name as append_dir's head.
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2024-10-02 14:38:35 +02:00 |
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ea898ca3c5
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Added file openning mode as input parameter. Now, mode can only take values in ['w','r+']
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2024-10-02 13:54:59 +02:00 |
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4f0361c6c5
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Removed construct_attributes_dict(attrs_obj) and replaced by {key: utils.to_serializable_dtype(val) for key, val in obj.attrs.items()}
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2024-10-01 10:42:20 +02:00 |
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1b0c666132
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Made two helper functions private by adding the prefix __
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2024-10-01 09:31:41 +02:00 |
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14a1d032b9
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Deleted annotate_root_dir(filename,annotation_dict: dict), and outsourced functionality to HDF5DataOpsManager.append_metadata() or .update_metadata() at obj_name = '/'
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2024-10-01 09:19:14 +02:00 |
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96500063fb
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Implemented metadata append, rename, delete, and update operations on the hdf5 manager object and refactored metadata update script based on yaml file to use said operations.
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2024-09-30 16:32:39 +02:00 |
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db6fcd03da
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Refactored a few function calls due to ranming changes in utils module
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2024-09-27 08:58:35 +02:00 |
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c992662a1f
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Renamed to_yaml() as serialize_metadata() and introduce input parameter output_format, which allows yaml or json.
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2024-09-26 16:23:09 +02:00 |
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02a7c4d834
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Performed a few function relocations and deletions from src/hdf5_lib.py into src/hdf5_ops.py and made a copy of previous version as src/hdf5_lib_part2.py
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2024-09-26 15:13:31 +02:00 |
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8f9e2fc594
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Moved is_structured_array() and to_serializable_dtype() to utils, ranamed a few functions and propagated changes to dependent modules.
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2024-09-26 14:03:11 +02:00 |
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7ab615019a
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Renamed take_yml_snapshot_of_hdf5_file func as to_yaml func
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2024-09-25 16:49:44 +02:00 |
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57d49a8db0
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Moved take_yml_snapshot_of_hdf5_file func and associted helper functions from hdf5_vis.py into hdf5_ops.py
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2024-09-25 16:42:44 +02:00 |
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7304655ba5
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Moved take_yml_snapshot_of_hdf5_file func and associted helper functions from hdf5_vis.py into hdf5_ops.py
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2024-09-25 16:40:16 +02:00 |
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32ba2a13cd
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Renamed make_dtype_yaml_compatible func as to_serializable_dtype func
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2024-09-25 16:36:50 +02:00 |
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3e143fb9c7
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Abstracted reusable steps in integration_sources as dima_pipeline.py and added functionality to make a collection of hdf5 files, where each represents an single experiment of campaign.
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2024-09-25 15:23:23 +02:00 |
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dd8fc1a906
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Robustified definition of path_to_input_dir arg or parameter by ensuring is always defined using forward slashes and then is normalized to the os specification. Improved dry run = True of copy directory func.
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2024-09-25 15:12:19 +02:00 |
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90d43a46f8
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Fixed instrument_dir estimation to be bottom up, ie, based on path to file. Otherwise, it does not work when dima used as submodule
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2024-09-19 15:47:11 +02:00 |
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0e354a0f14
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Moved src/metadata_review_lib.py pipelines/metadata_revision.py
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2024-09-17 16:55:22 +02:00 |
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de859102ab
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Moved src/data_integration_lib.py -> pipelines/data_integration.py
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2024-09-17 15:32:23 +02:00 |
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59861c3aa8
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Refactored code into functions to parse and validate yaml condif file and to perform specified data integration task using a pipeline like software structure.
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2024-09-17 15:28:11 +02:00 |
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7b3b453db1
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Major update. Remove file filtering option and outputname input arg. The output name is now the same as the path_to_input_dir + .h5. By default, the hdf5 writer preserves second level subdirectories and the rest are flattend. dir filtering is outsource to copy_dir_with_constraints from utils-
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2024-09-16 16:35:09 +02:00 |
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eec38f61d7
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Restructured a bit to include the default case of copying an imnput directory without any constraints. Also, added dry_run input argument that returns a path to files dict representation of output directory without making an actual copy. Useful when input directory is already safe to work with directly
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2024-09-16 15:38:30 +02:00 |
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6d91c043f8
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Renamed parameter 'input_file_system_path' to 'path_to_input_directory' for clarity.
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2024-09-16 14:24:55 +02:00 |
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85b4909713
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Fixed import statement
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2024-09-13 15:11:25 +02:00 |
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0f913e5002
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move def get_parent_child_relationships(file: h5py.File) from ..._vis.py to ..._ops.py
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2024-09-13 14:59:11 +02:00 |
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4813359a4f
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src/hdf5_data_extraction.py -> src/hdf5_ops.py
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2024-09-13 14:55:12 +02:00 |
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4525c1ba04
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Added new method to retreive metadata from h5file at a given obj path
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2024-09-13 14:52:07 +02:00 |
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3e1a46ebc7
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Fixed import statement after module's relocation
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2024-08-23 16:23:57 +02:00 |
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926dc9208a
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Modified to use filereader_registry.py.
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2024-08-23 16:10:23 +02:00 |
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1e0da55abc
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Removed and splitted into instruments/readers/filereader_registry.py instruments/readers/g5505_text_reader.py instruments/readers/xps_ibw_reader.py
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2024-08-23 16:09:04 +02:00 |
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0a58e86bcb
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Split instruments/readers/g5505_file_reader.py into a fileregistry.py and independent file readers. This is to improve instrument modularity and additions
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2024-08-23 16:06:44 +02:00 |
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cfae414b0e
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Renamed to reflect better the functionality of the file
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2024-08-23 15:50:14 +02:00 |
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b499ef2845
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Integrated copy h5 file into group functionality, imported from g5505_file_reader
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2024-08-23 15:47:04 +02:00 |
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7ad4e686a7
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Moved copy_file_in_group() into hdf5_lib.py because it is not really doing the same role of all filereaders
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2024-08-23 15:45:32 +02:00 |
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33ad9acdd4
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Moved all yaml files with dictionary terms for each instrument to dictionaries folder
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2024-08-23 14:32:23 +02:00 |
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f20e02d62f
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Added ACSM_TOFWARE metadata descriptions
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2024-08-23 14:23:32 +02:00 |
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17dd1f1864
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Modified import statements to account for reader module's relocation.
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2024-08-23 13:27:26 +02:00 |
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a33e2b681f
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Fixed a few import dependencies after relocating this file.
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2024-08-23 10:57:13 +02:00 |
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e76ed79f1e
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Moved src/g5505_file_reader.py -> instruments/readers/g5505_file_reader.py to increase modularity with respect to new intrument additions.
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2024-08-23 10:11:29 +02:00 |
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b22b0e94e4
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Moved src/g5505_utils.py to utils/g5505_utils.py
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2024-08-23 07:27:39 +02:00 |
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9d917226af
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Moved get_parent_relationships func into hdf5_vis.py and cleaned up unused import statements
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2024-08-22 09:50:26 +02:00 |
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da6cca1632
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Moved get_parent_child_relationships() funct from hdf5_lib.py tinto hdf5_vis.py to avoid circular dependency between the lower level and higher level module. Thus removed also src.hdf5_lib.py import statement.
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2024-08-22 09:47:57 +02:00 |
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d6dce9a392
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Implemented method for appending new attributes to an specific object.
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2024-08-16 09:32:58 +02:00 |
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ea13f2b71b
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Implemented method to reformat a given column in a datatable holding datetime info into a desired datetime format. During data integration this will serve to normalize datatime formats across data tables
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2024-08-16 08:08:28 +02:00 |
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3fc96a89d2
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Added method to reformat columns containing datetime byte strings into a desired datetime formated object
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2024-08-14 16:22:28 +02:00 |
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