 florez_j
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11ca454b94
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Removed bacause some of the functionalities have been outsourced to other modules src/hdf5_ops.py and src/hdf5_writer.py
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2024-11-26 11:55:06 +01:00 |
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florez_j
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5c61e2391a
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Update to DIMA package path resolution from file.
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2024-11-24 19:45:18 +01:00 |
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florez_j
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1174ffc8b8
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Commented out metadata info about group members for a given group. This is to simplify yaml or json representation of the metadata.
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2024-11-24 15:57:54 +01:00 |
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florez_j
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967be876d1
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Moved func create_hdf5_file_from_dataframe() from hdf5_lib_part2 into hdf5_write.py
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2024-11-24 11:30:08 +01:00 |
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florez_j
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0330773f08
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Moved read_mtable_as_dataframe(filename) to src/hdf5_ops.py
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2024-11-24 11:03:44 +01:00 |
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florez_j
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b24d33ab15
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Check whether h5 file being written exists. If so, we do not overwrite it because it may be underdoing refinement, changes or updates, for archiving, sharing, or publishing.
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2024-11-24 10:38:13 +01:00 |
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florez_j
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6701bc06ad
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Added read_mtable_as_dataframe(filename) back so that jupyter notebook can use it to demonstrate some functionality
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2024-11-23 16:31:29 +01:00 |
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florez_j
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1be4b8493a
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Improved progress description stdout
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2024-11-10 18:21:00 +01:00 |
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florez_j
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e2fec03d4a
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Included cli commands update and serialize to simplify running metadata revision pipeline.
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2024-10-29 07:56:43 +01:00 |
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florez_j
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cc96672245
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Moved git related operations from pipelines/ to src/git_ops.py
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2024-10-28 16:30:34 +01:00 |
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florez_j
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69b73c26b0
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Corrected import statements due to dependency name changes
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2024-10-17 16:52:42 +02:00 |
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florez_j
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7c60193aa6
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Renamed module: src/hdf5_lib.py -> src/hdf5_writer.py
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2024-10-17 10:53:51 +02:00 |
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florez_j
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44073e3816
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Replaced read_dataset_from_hdf5file(hdf5_file_path, dataset_path) with HDF5DataOpsManager.extract_dataset_as_dataframe(self,dataset_name)
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2024-10-17 10:46:19 +02:00 |
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florez_j
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2a9d69c757
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Robustified metadata and dataset extraction methods by requiring explicit load of file obj before their use. Renamed a few functions and fixed types in print statements.
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2024-10-10 11:28:23 +02:00 |
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florez_j
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6be3b31247
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Renamed open_file() --> load_file_obj() and close_file() --> unload_file_obj() to focus more on the management operations on the files that actual file handling operations.
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2024-10-10 10:47:44 +02:00 |
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florez_j
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568f747a69
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Robustifed metadata revision methods with error detection conditions and try-except statements. Metadata revision methods now do not have the capability of opening the file.
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2024-10-10 10:39:10 +02:00 |
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florez_j
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fe96134383
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Fixed bug in HDF5DataOpsManager.append_dataset() and added 'creation_date' metadata attribute when instrument (groups) are created.
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2024-10-09 16:06:44 +02:00 |
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florez_j
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c321a17943
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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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florez_j
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89e9dd9ab1
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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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florez_j
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9b5d777a5b
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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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florez_j
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aad0a7c3fb
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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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florez_j
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4420f81642
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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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florez_j
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4d48e84e50
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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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florez_j
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8cd4b7d925
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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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florez_j
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6f5d4adcee
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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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florez_j
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96dad0bfb1
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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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florez_j
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85b0e5ab74
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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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florez_j
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a92660049f
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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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florez_j
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a57e46d89c
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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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florez_j
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7b221599d8
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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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florez_j
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1e93a2c552
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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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florez_j
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10554fc41e
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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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florez_j
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1e1499c28a
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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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florez_j
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9eeb9d6380
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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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florez_j
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07401c895f
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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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florez_j
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2dd033bcb3
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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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florez_j
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d63f522588
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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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florez_j
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7a9f7a8c59
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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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florez_j
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cc0adfca62
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Fixed import statement
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2024-09-13 15:11:25 +02:00 |
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florez_j
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4974246522
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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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florez_j
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b42482069c
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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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florez_j
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e8e2473ebe
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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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florez_j
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96a2e96b6a
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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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florez_j
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e4b04b4484
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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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florez_j
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d985115125
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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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florez_j
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18165eca1a
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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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florez_j
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a0f44a1f4b
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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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florez_j
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1112a214e9
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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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florez_j
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d7fc38abd9
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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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florez_j
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05d1133e32
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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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