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add examples
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‎docs/example_notebooks/export_to_sqlite_netcdf.ipynb‎

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},
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"source": [
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"# Example on how to Export\n",
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"## from a Local SQLite database to an shared SQLite database or netcdf file"
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"## from a Local SQLite database to an shared SQLite database or netcdf/CSV file"
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]
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{
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},
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"outputs": [],
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"source": [
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"import pymongo\n",
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"import tempfile\n",
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"import os\n",
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"import time\n",
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"import pandas as pd\n",
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"from qdatalib.tolib import Qdatalib\n",
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"from qcodes.tests.instrument_mocks import DummyInstrument, DummyInstrumentWithMeasurement\n",
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"from qcodes import load_or_create_experiment, initialise_or_create_database_at\n",
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"from qcodes.utils.dataset.doNd import do1d, do2d\n",
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"from qcodes.dataset.plotting import plot_dataset"
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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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"slideshow": {
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"slide_type": "skip"
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}
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},
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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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"[WinError 183] Cannot create a file when that file already exists: 'C:\\\\Users\\\\rbcma\\\\AppData\\\\Local\\\\Temp\\\\qdatalib'\n"
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]
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}
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],
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"source": [
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"# Can be ignored, Setting up temporary files and folder to be used in the example\n",
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"TEMP_PATH = tempfile.gettempdir()\n",
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"my_path = os.path.join(TEMP_PATH,'qdatalib')\n",
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"try:\n",
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" os.mkdir(my_path)\n",
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"except Exception as e:\n",
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" print(e)\n",
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" \n",
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"\n",
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"\n"
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"from qcodes.utils.dataset.doNd import do1d, do2d"
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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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"slideshow": {
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"slide_type": "slide"
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}
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},
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"metadata": {},
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"source": [
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"## To use QDataLib we first need a conextion to a MongoDB database"
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"### Instantiate Qdatalib\n",
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"To use Qdatalib you need an instance. If you have not setup Qdatalib yet see the example: setting_up_qdatalib"
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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": 3,
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"execution_count": 2,
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"metadata": {
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"slideshow": {
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"slide_type": "-"
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}
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},
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"outputs": [],
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"source": [
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"client = pymongo.MongoClient(\"mongodb+srv://rbch:test4RBCH@test.2smqf.mongodb.net/testdb?retryWrites=true&w=majority\")\n",
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"db = client['testdb']\n",
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"collection = db[\"testcol\"]"
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"qdatalib = Qdatalib()\n",
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"local_path_db = qdatalib.db_local"
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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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"slideshow": {
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"slide_type": "slide"
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}
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},
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"source": [
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"## Then we need a and instace of the class Qdatalib\n",
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"\n",
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"### Passing\n",
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"- collection: The collection used to keep track of your data files\n",
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"- db_local: The SQLite database to export from\n",
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"- db_shared: The SQLite database to export to\n",
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"- shared_dir: The Directory where other dataformats should be stored \n"
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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": 4,
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"metadata": {
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"slideshow": {
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"slide_type": "-"
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}
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},
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"outputs": [],
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"metadata": {},
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"source": [
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"shared_dir = \"C:\\\\Users\\\\rbcma\\\\Spin Qubit Dropbox\\\\qdatalib QDev\\\\Test\"\n",
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"shared_path_db = os.path.join(shared_dir,'shared.db')\n",
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"local_path_db = os.path.join(my_path, 'qdatalib_tutorial.db')\n",
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"\n",
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"qdatalib = Qdatalib(collection,\n",
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" local_path_db,\n",
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" shared_path_db,\n",
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" shared_dir)"
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"#### To illustrate we run a dummy experiment"
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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": 5,
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"metadata": {
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"slideshow": {
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"slide_type": "slide"
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}
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},
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"outputs": [],
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"source": [
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"#Setting up a Dummy experiment\n",
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"\n",
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"initialise_or_create_database_at(local_path_db)\n",
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"exp = load_or_create_experiment(experiment_name='qdatalib',\n",
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" sample_name=\"no sample\")\n",
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"dac = DummyInstrument('dac', gates=['ch1', 'ch2'])\n",
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"dmm = DummyInstrumentWithMeasurement('dmm', setter_instr=dac)"
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]
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},
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{
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"cell_type": "markdown",
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"execution_count": 3,
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"metadata": {
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"slideshow": {
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"slide_type": "slide"
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}
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},
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"source": [
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"#### To illustrate we run a dummy experiment\n"
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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": 6,
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"metadata": {
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"slideshow": {
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"slide_type": "-"
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}
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},
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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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"Starting experimental run with id: 13. \n"
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"Upgrading database; v0 -> v1: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v1 -> v2: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 500.99it/s]\n",
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"Upgrading database; v2 -> v3: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v3 -> v4: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v4 -> v5: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 334.15it/s]\n",
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"Upgrading database; v5 -> v6: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v6 -> v7: 100%|██████████████████████████████████████████████████████| 1/1 [00:00<00:00, 90.95it/s]\n",
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"Upgrading database; v7 -> v8: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 501.11it/s]\n",
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"Upgrading database; v8 -> v9: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 334.05it/s]\n"
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]
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}
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],
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"source": [
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"initialise_or_create_database_at(local_path_db)\n",
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"exp = load_or_create_experiment(experiment_name='qdatalib',\n",
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" sample_name=\"no sample\")\n",
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"dac = DummyInstrument('dac', gates=['ch1', 'ch2'])\n",
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"dmm = DummyInstrumentWithMeasurement('dmm', setter_instr=dac)\n",
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"\n",
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"data = do1d(dac.ch1, 0, 10, 10, 0.01, dmm.v1, dmm.v2, do_plot=False)\n",
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"run_id = data[0].run_id\n"
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"run_id = data[0].run_id"
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]
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},
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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": 7,
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"execution_count": 5,
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"metadata": {
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"slideshow": {
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"slide_type": "-"
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"output_type": "stream",
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"text": [
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"Upgrading database; v0 -> v1: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v1 -> v2: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 251.10it/s]\n",
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"Upgrading database; v1 -> v2: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 334.13it/s]\n",
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"Upgrading database; v2 -> v3: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v3 -> v4: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v4 -> v5: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 200.44it/s]\n",
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"Upgrading database; v4 -> v5: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 501.11it/s]\n",
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"Upgrading database; v5 -> v6: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v6 -> v7: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 143.24it/s]\n",
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"Upgrading database; v7 -> v8: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 250.56it/s]\n",
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"Upgrading database; v8 -> v9: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 200.59it/s]\n"
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"Upgrading database; v6 -> v7: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 178.75it/s]\n",
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"Upgrading database; v7 -> v8: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 501.29it/s]\n",
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"Upgrading database; v8 -> v9: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 333.99it/s]\n"
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]
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}
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],
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"source": [
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"scientist = 'John doe'\n",
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"tag = 'double dot',\n",
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"note = 'This happened',\n",
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"dict_exstra = {'my_field': 'Group K', 'my_Score': 2, 'Presented':'group meeting June 24, 2021'}\n",
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"dict_exstra = {'my_field': 'Group NB', 'my_Score': 2, 'Presented':'group meeting June 24, 2021'}\n",
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"\n",
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"\n",
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"qdatalib.extract_run_into_db_and_catalog_by_id(run_id=run_id,\n",
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" scientist=scientist,\n",
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" tag=tag,\n",
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" note=note,\n",
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" dict_exstra = {'my_field': 'Group DD', 'my_Score': 2, 'Presented':'group meeting June 24, 2021'})"
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" dict_exstra = dict_exstra)"
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]
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},
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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": 8,
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"execution_count": 6,
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"metadata": {
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"slideshow": {
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"slide_type": "-"
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" dict_exstra = dict_exstra)"
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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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"We can now setup and run another experiment, exporting to the same mongodb database "
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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": 7,
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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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"Upgrading database; v0 -> v1: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v1 -> v2: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 501.35it/s]\n",
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"Upgrading database; v2 -> v3: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v3 -> v4: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v4 -> v5: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 334.02it/s]\n",
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"Upgrading database; v5 -> v6: : 0it [00:00, ?it/s]\n",
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"Upgrading database; v6 -> v7: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 195.98it/s]\n",
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"Upgrading database; v7 -> v8: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 334.05it/s]\n",
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"Upgrading database; v8 -> v9: 100%|█████████████████████████████████████████████████████| 1/1 [00:00<00:00, 334.29it/s]\n",
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"Starting experimental run with id: 1. \n"
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]
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}
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],
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"source": [
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"db_local = os.path.join(qdatalib.lib_dir, 'qdatalib_localB.db')\n",
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"db_shared = os.path.join(qdatalib.lib_dir, 'sharedB.db')\n",
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"qdatalib.set_db_local(db_local)\n",
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"\n",
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"initialise_or_create_database_at(db_local)\n",
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"exp = load_or_create_experiment(experiment_name='qdatalibB',\n",
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" sample_name=\"no sampleB\")\n",
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"\n",
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"\n",
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"data = do1d(dac.ch1, 0, 10, 10, 0.01, dmm.v1, dmm.v2, do_plot=False)\n",
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"run_id = data[0].run_id\n",
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"\n",
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"scientist = 'Jane doe'\n",
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"tag = 'sigle dot',\n",
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"note = 'This happened again',\n",
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"dict_exstra = {'my_field': 'Group C', 'my_Score': 10, 'Presented':'group meeting July 24, 2021'}\n",
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"\n",
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"\n",
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"qdatalib.extract_run_into_db_and_catalog_by_id(run_id=run_id,\n",
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" scientist=scientist,\n",
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" tag=tag,\n",
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" note=note,\n",
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" dict_exstra = dict_exstra)"
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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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"Finaly we can also export to csv"
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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": 8,
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"metadata": {},
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"outputs": [],
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"source": [
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"qdatalib.extract_run_into_csv_and_catalog(run_id=run_id,\n",
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" scientist=scientist,\n",
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" tag=tag,\n",
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" note=note,\n",
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" dict_exstra = dict_exstra)"
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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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