5505-public/dima
2
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Rerun jupyternotebooks to check their functionality after relocating them to notebooks. OpenBis related python scripts still need to be tested.

Browse Source
This commit is contained in:
florez_j
2024-11-24 10:45:40 +01:00
parent 02ded9c11a
commit c257ab6072
6 changed files with 7402 additions and 85 deletions
Download Patch File Download Diff File Expand all files Collapse all files

44
notebooks/example_workflow_metadata_annotation.ipynb
View File

@ -23,11 +23,29 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Imports successful!\n"
]
}
],
"source": [
"import src.metadata_review_lib as metadata_annotation\n",
"import src.hdf5_vis as hdf5_vis\n",
"import os"
"import os\n",
"from nbutils import add_project_path_to_sys_path\n",
"\n",
"\n",
"# Add project root to sys.path\n",
"add_project_path_to_sys_path()\n",
"\n",
"try:\n",
" import src.hdf5_ops as hdf5_ops\n",
" import pipelines.metadata_revision as metadata_revision\n",
" print(\"Imports successful!\")\n",
"except ImportError as e:\n",
" print(f\"Import error: {e}\")"
]
},
{
@ -46,7 +64,7 @@
"metadata": {},
"outputs": [],
"source": [
"hdf5_file_path = \"output_files/kinetic_flowtube_study_2023-06-29_LuciaI.h5\""
"hdf5_file_path = \"../output_files/collection_kinetic_flowtube_study_LuciaI_2022-01-31_2023-06-29/kinetic_flowtube_study_LuciaI_2023-06-29.h5\""
]
},
{
@ -62,11 +80,19 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The YAML file representation output_files/collection_kinetic_flowtube_study_LuciaI_2022-01-31_2023-06-29/kinetic_flowtube_study_LuciaI_2023-06-29.json of the HDF5 file output_files/collection_kinetic_flowtube_study_LuciaI_2022-01-31_2023-06-29/kinetic_flowtube_study_LuciaI_2023-06-29.h5 was created successfully.\n"
]
}
],
"source": [
"yaml_file_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(hdf5_file_path)\n",
"yaml_file_path = hdf5_ops.serialize_metadata(hdf5_file_path,output_format='json')\n",
"\n",
"if os.path.exists(yaml_file_path):\n",
" print(f'The YAML file representation {yaml_file_path} of the HDF5 file {hdf5_file_path} was created successfully.')"
@ -118,7 +144,7 @@
"outputs": [],
"source": [
"\n",
"metadata_annotation.update_hdf5_file_with_review(hdf5_file_path,yaml_file_path)"
"metadata_revision.update_hdf5_file_with_review(hdf5_file_path,yaml_file_path)"
]
}
],