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f483e8d7fe
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Updated instrument dictionaries with variable descriptor names aligned with CF metadata conventions.
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2024-11-25 15:49:49 +01:00 |
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85d44d71d6
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Attempt to dynamically resolve path to dima package, when excecuted from command line.
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2024-11-24 17:37:38 +01:00 |
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6dc89d34fe
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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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60f9278f10
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Reimplemented code snippet using hdf5_Writer module
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2024-11-24 11:32:26 +01:00 |
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3db2eeb041
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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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2740330709
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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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ff31c14f92
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Removed logs/ folder. This is usually created locally to trace certain file copying, transfer and conversion processes.
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2024-11-24 10:51:05 +01:00 |
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01767340f9
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Rerun jupyternotebooks to check their functionality after relocating them to notebooks. OpenBis related python scripts still need to be tested.
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2024-11-24 10:45:40 +01:00 |
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7708153a62
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Add hidden.py to the list. This file may contain sensitive information is only to be accessed locally or from a secure location.
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2024-11-24 10:41:32 +01:00 |
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53fae27472
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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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d10786a534
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Add utility functions add_project_path_to_sys_path() to set up path to DIMA's modules dynamically.
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2024-11-24 10:08:19 +01:00 |
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058b82ff88
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Moved demos .py to notebooks. Note: Maybe turn them to jupyternotebooks for consistency
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2024-11-24 07:49:50 +01:00 |
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2988d816af
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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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ac80b9a3ca
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Implemented sanitize dataframe function to deal with 'O' which may have numbers or strings detected as string types. Then we use it prior to convert dataframe into structured numpy array.
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2024-11-23 16:28:49 +01:00 |
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ca23e363c9
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Moved to notebooks/
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2024-11-23 12:29:55 +01:00 |
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feee8762ed
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Moved to notebooks/
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2024-11-23 12:16:13 +01:00 |
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cc7ad749ca
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Moved to notebooks/ to improve repo organization
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2024-11-23 12:06:27 +01:00 |
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13cb5476b1
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Moved data integration ipynb to notebooks folder to improve readability
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2024-11-23 11:24:28 +01:00 |
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05f16bf717
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Added .pkl extension in the list of admissible file extensions
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2024-11-21 11:47:41 +01:00 |
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59e910a0f9
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Modified logger setup to create monthly logs
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2024-11-21 11:46:11 +01:00 |
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90ae93c124
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Added a logs/ and envs/ folder to gitignore.
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2024-11-21 11:44:38 +01:00 |
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870d60a789
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Improved progress description stdout
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2024-11-10 18:21:00 +01:00 |
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c866ce8ee9
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Fixed command line interface bug
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2024-11-10 18:19:59 +01:00 |
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83b4a12e8b
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Major code refactoring and simplifications to enhance modularity. Included a command line interface.
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2024-11-01 09:52:41 +01:00 |
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2ae8deaf64
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Renamed the input argument yaml_review_file as review_yaml_file.
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2024-11-01 09:51:12 +01:00 |
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29c6d86583
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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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71b7091fe7
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Fixed bug: to_serializable_dtype() did not identify correctly dtype of array's entries with object dtype
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2024-10-28 18:49:22 +01:00 |
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e01147d03a
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Removed unused import statements
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2024-10-28 16:37:32 +01:00 |
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c0ec7e9b26
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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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66e236bd5d
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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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a8ceffba8b
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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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8129949db9
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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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d49e7ae9d5
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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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13d65a7383
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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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9a76b3a01a
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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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5cc409f882
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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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51e8e6ae66
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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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5b338c8212
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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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507454ee91
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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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1e5581769b
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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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81e3cc58ca
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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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800a5aca49
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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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47f095bdc8
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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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cdb0c612ad
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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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8ea111a0c7
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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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ecb0425a20
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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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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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74a78b9534
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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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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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