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74633adf7f
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Removed unused import statements
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2024-10-28 16:37:32 +01:00 |
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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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15b0ff3cc4
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Added function to validate review yaml file, and updated update_hdf5_with_review function
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2024-10-28 16:20:28 +01:00 |
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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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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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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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f1b2c64f66
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Fixed bug when file reader not available. File reader registry now returns a reade that maps input to None.
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2024-10-14 16:03:03 +02:00 |
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2a330fcf92
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Added 'filename_format' attribute to YAML schema. It takes as value a string of comma separated keys from available attributes in YAML file.
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2024-10-14 16:01:24 +02:00 |
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1954542031
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Fixed bug introduce in logger due to invalid date naming replace : with -
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2024-10-10 14:29:36 +02:00 |
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ea82af2cd5
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Cleaned up import statements and comment out path append operations
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2024-10-10 14:27:50 +02:00 |
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7d94ce29dd
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Attempt to initialize dima/utils as a module
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2024-10-10 11:53:27 +02:00 |
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1c2588d85f
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Attemp to initialize dima as a module
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2024-10-10 11:43:02 +02:00 |
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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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7653e982a4
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Updated function dependencies to reflect changes made to hdf5_ops.py
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2024-10-10 11:02:05 +02:00 |
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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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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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31c9db98ca
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Changed datetime format output of created_at() function as '%Y-%m-%d %H:%M:%S.%f'
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2024-10-09 16:07:40 +02:00 |
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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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7c683f96a1
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Merge branch 'main' of https://gitlab.psi.ch/5505/dima
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2024-10-07 16:19:10 +02:00 |
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9a3bf77f37
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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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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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dc7f156367
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Updated README.md with guide for intrument dependent file reader extensions and updated TODO.md with pending tasks.
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2024-10-03 11:31:51 +02:00 |
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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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098a79531c
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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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01b39b4c02
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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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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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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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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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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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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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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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afe31288a0
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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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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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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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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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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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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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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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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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df2f7b3de6
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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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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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0dbec94374
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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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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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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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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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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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9c641c0dae
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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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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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cc0adfca62
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Fixed import statement
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2024-09-13 15:11:25 +02:00 |
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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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