161 lines
6.8 KiB
Plaintext
161 lines
6.8 KiB
Plaintext
{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Import libraries and modules\n",
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"\n",
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"* Excecute (or Run) Cell"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"import sys\n",
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"import os\n",
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"root_dir = os.path.abspath(os.curdir)\n",
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"sys.path.append(root_dir)\n",
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"\n",
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"import src.metadata_review_lib as metadata_review_lib"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Step 1: initialize metadata review.\n",
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"\n",
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"* Specify hdf5 file whose metadata is to be reviewed by editing the string variable `hdf5_file_path`.\n",
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"* Edit reviewer attributes, i.e., the dict variable `reviewer_attrs` with your own initials and role.\n",
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"* Excecute Cell."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Create branch metadata-review-by-NG\n",
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"\n"
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]
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},
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{
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"ename": "ValueError",
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"evalue": "('Please checkout the branch: ', 'data-owner-review-by-NG', \" via Git Bash Terminal while in the project's directory\")",
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"output_type": "error",
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"traceback": [
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"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[1;31mValueError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[1;32mIn[2], line 12\u001b[0m\n\u001b[0;32m 7\u001b[0m reviewer_attrs \u001b[38;5;241m=\u001b[39m {\u001b[38;5;124m'\u001b[39m\u001b[38;5;124minitials\u001b[39m\u001b[38;5;124m'\u001b[39m: \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mNG\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[0;32m 8\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtype\u001b[39m\u001b[38;5;124m'\u001b[39m: \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdata-owner\u001b[39m\u001b[38;5;124m'\u001b[39m}\n\u001b[0;32m 10\u001b[0m \u001b[38;5;66;03m#output_filename_path, output_yml_filename_path = hdf5_lib.main()\u001b[39;00m\n\u001b[1;32m---> 12\u001b[0m review_yaml_file_path \u001b[38;5;241m=\u001b[39m \u001b[43mmetadata_review_lib\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfirst_initialize_metadata_review\u001b[49m\u001b[43m(\u001b[49m\u001b[43mhdf5_file_path\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mreviewer_attrs\u001b[49m\u001b[43m)\u001b[49m \n\u001b[0;32m 14\u001b[0m \u001b[38;5;28mprint\u001b[39m(review_yaml_file_path) \n",
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"File \u001b[1;32mc:\\Users\\florez_j\\Documents\\GitLab\\functionspython\\src\\metadata_review_lib.py:89\u001b[0m, in \u001b[0;36mfirst_initialize_metadata_review\u001b[1;34m(hdf5_file_path, reviewer_attrs)\u001b[0m\n\u001b[0;32m 87\u001b[0m curr_branch \u001b[38;5;241m=\u001b[39m subprocess\u001b[38;5;241m.\u001b[39mrun(current_branch_command,capture_output\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,text\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,check\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m 88\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m branch_name \u001b[38;5;129;01min\u001b[39;00m curr_branch\u001b[38;5;241m.\u001b[39mstdout:\n\u001b[1;32m---> 89\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPlease checkout the branch: \u001b[39m\u001b[38;5;124m\"\u001b[39m,branch_name,\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m via Git Bash Terminal while in the project\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124ms directory\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m 91\u001b[0m \u001b[38;5;66;03m# Check if review file already exists and then check if it is still untracked\u001b[39;00m\n\u001b[0;32m 92\u001b[0m review_yaml_file_path \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mreview/\u001b[39m\u001b[38;5;124m\"\u001b[39m,filename\u001b[38;5;241m+\u001b[39mYAML_EXT)\n",
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"\u001b[1;31mValueError\u001b[0m: ('Please checkout the branch: ', 'data-owner-review-by-NG', \" via Git Bash Terminal while in the project's directory\")"
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]
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}
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],
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"source": [
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"\n",
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"#hdf5_file_path = \"output_files/unified_file_smog_chamber_2024-03-25_UTC-OFST_+0100_NG.h5\"\n",
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"#yml_file_path = \"output_files/unified_file_smog_chamber_2024-03-25_UTC-OFST_+0100_NG.yaml\"\n",
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"\n",
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"hdf5_file_path = \"output_files/unified_file_smog_chamber_2024-04-03_UTC-OFST_+0200_NG.h5\"\n",
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"yml_file_path = \"output_files/unified_file_smog_chamber_2024-04-03_UTC-OFST_+0200_NG.yaml\"\n",
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"\n",
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"reviewer_attrs = {'initials': 'NG',\n",
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" 'type': 'data-owner'}\n",
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"\n",
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"#output_filename_path, output_yml_filename_path = hdf5_lib.main()\n",
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"\n",
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"review_yaml_file_path = metadata_review_lib.first_initialize_metadata_review(hdf5_file_path, reviewer_attrs) \n",
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"\n",
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"print(review_yaml_file_path) "
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Step 2: Submit metadata review. \n",
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"\n",
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"* Edit yaml file in review folder and save changes\n",
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"* Excecute Cell."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"metadata_review_lib.second_submit_metadata_review(review_yaml_file_path,reviewer_attrs)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Step 3: Update hdf5 file metadata w/ submitted review yaml file.\n",
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"\n",
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"* Make sure previous step was carried out properly.\n",
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"* Excecute Cell."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"\n",
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"metadata_review_lib.third_update_hdf5_file_with_review(hdf5_file_path, review_yaml_file_path, reviewer_attrs)\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Step 4: Complete data-owner review. Update remote repository\n",
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"\n",
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"* Excecute Cell."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"metadata_review_lib.fourth_complete_metadata_review(reviewer_attrs)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "test_atmos_chem_env",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}
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