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Merge pull request #329 from Exabyte-io/chore/SOF-7908
chore/SOF 7908
2 parents 3712fa8 + 8ca2bdc commit 083612e

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‎README.md‎

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@@ -8,7 +8,7 @@ Notebooks demonstrating the Mat3ra REST API, in roughly the order a new user sho
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| Folder | Notebook | Description |
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|--------|----------|-------------|
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| [system](examples/system/) | [Get Authentication Params](examples/system/get_authentication_params.ipynb) | Programmatically find your user ID and access token. |
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| [system](examples/system/) | [Get Authentication Params](examples/system/get_authentication_params.ipynb) | Authenticate via OIDC and inspect account credentials. |
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| [material](examples/material/) | [Get Materials by Formula](examples/material/get_materials_by_formula.ipynb) | Query materials stored on your account by chemical formula. |
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| [material](examples/material/) | [Create Material](examples/material/create_material.ipynb) | Generate a material in [JSON format](https://docs.mat3ra.com/materials/data/) and upload it to your account. |
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| [material](examples/material/) | [Import Materials from POSCAR](examples/material/upload_materials_from_file_poscar.ipynb) | Import materials directly from POSCAR files. |
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1. Assert an existing Mat3ra.com account. Examples require an account to run. New users can register [here](https://platform.mat3ra.com/register) to obtain one.
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2. Open [settings](src/py/mat3ra/notebooks_utils/core/api/settings.json) and adjust it to provide the API authentication parameters. See the [corresponding example](examples/system/get_authentication_params.ipynb) to learn how to obtain the authentication parameters. It is also possible to generate an API token by logging in to [Mat3ra platform](https://platform.mat3ra.com/), navigating to the Account Preferences, and clicking the 'Generate new token' button under API Tokens. More details can be found [here](https://docs.mat3ra.com/accounts/ui/preferences/api/).
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2. Open the desired example notebook and run all cells. Authentication uses OIDC device flow via `await authenticate()` — a browser popup opens for login. On JupyterLite (platform-embedded notebooks), credentials are injected automatically.
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3. Open the desired example notebook, adjust it as necessary and run. One can speed up the notebooks execution after running the [Get Authentication Params](examples/system/get_authentication_params.ipynb) one by reusing the kernel from the first notebook.
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3. Optionally, for local Jupyter without OIDC, set legacy API token values in [settings.json](src/py/mat3ra/notebooks_utils/core/api/settings.json). See [Get Authentication Params](examples/system/get_authentication_params.ipynb) for details. API tokens can also be generated in [Account Preferences](https://docs.mat3ra.com/accounts/ui/preferences/api/) on the platform.
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<img src="images/reusable-kernel.png" width="250px" />
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NOTE: The Materials Project API key should be obtained from [https://legacy.materialsproject.org/open](https://legacy.materialsproject.org/open).
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NOTE: The Materials Project API key should be set in `settings.json` and obtained from [https://legacy.materialsproject.org/open](https://legacy.materialsproject.org/open).
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## Contribute

‎examples/job/create_and_submit_job.ipynb‎

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{
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"cells": [
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {
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"id": "4iM5tpoN3sR3"
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},
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"source": [
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"<a href=\"https://colab.research.google.com/github/Exabyte-io/api-examples/blob/dev/examples/job/create_and_submit_job.ipynb\" target=\"_parent\">\n",
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"<img alt=\"Open in Google Colab\" src=\"https://user-images.githubusercontent.com/20477508/128780728-491fea90-9b23-495f-a091-11681150db37.jpeg\" width=\"150\" border=\"0\">\n",
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"</a>"
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]
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {
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"id": "mHaR0BOJ3sR5"
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},
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"source": [
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"# Overview\n",
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"\n",
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"This example demonstrates how to create and submit a job via [Job](https://docs.mat3ra.com/api/Job/put_jobs_create) endpoints."
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]
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"source": "# Overview\n\nThis example demonstrates how to create and submit a job via [Job](https://docs.mat3ra.com/api/Job/put_jobs_create) endpoints."
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {
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"id": "i-kHKlAM3sR5"
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},
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"source": [
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"# Complete Authorization Form and Initialize Settings\n",
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"\n",
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"This will also determine environment and set all environment variables. We determine if we are using Jupyter Notebooks or Google Colab to run this tutorial.\n",
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"\n",
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"If you are running this notebook from Google Colab, Colab takes ~1 min to execute the following cell.\n",
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"\n",
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"ACCOUNT_ID and AUTH_TOKEN - Authentication parameters needed for when making requests to [Mat3ra.com's API Endpoints](https://docs.mat3ra.com/rest-api/endpoints/).\n",
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"\n",
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"ORGANIZATION_ID - Authentication parameter needed for when working with collaborative accounts https://docs.mat3ra.com/collaboration/organizations/overview/\n",
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"\n",
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"> <span style=\"color: orange\">**NOTE**</span>: If you are running this notebook from Jupyter, the variables ACCOUNT_ID, AUTH_TOKEN, and ORGANIZATION_ID should be set in the file [settings.json](../../utils/settings.json) if you need to use these variables. To obtain API token parameters, please see the following link to the documentation explaining how to get them: https://docs.mat3ra.com/accounts/ui/preferences/api/"
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]
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"source": "## Authenticate and initialize API client\n\n### Authenticate\nAuthenticate in the browser (OIDC device flow) or via JupyterLite host injection. Credentials are stored in environment variables.\n\n### Initialize API client\nCreate an authenticated API client and resolve the owner account ID."
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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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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"# @title Authorization Form\n",
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"ACCOUNT_ID = \"ACCOUNT_ID\" # @param {type:\"string\"}\n",
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"AUTH_TOKEN = \"AUTH_TOKEN\" # @param {type:\"string\"}\n",
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"ORGANIZATION_ID = \"ORGANIZATION_ID\" # @param {type:\"string\"}\n",
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"\n",
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"import os\n",
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"import sys\n",
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"\n",
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"if \"COLAB_JUPYTER_IP\" in os.environ:\n",
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" os.environ.update(\n",
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" dict(\n",
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" ACCOUNT_ID=ACCOUNT_ID,\n",
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" AUTH_TOKEN=AUTH_TOKEN,\n",
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" ORGANIZATION_ID=ORGANIZATION_ID,\n",
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" )\n",
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" )\n",
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"\n",
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" !GIT_BRANCH=\"dev\"; export GIT_BRANCH; curl -s \"https://raw.githubusercontent.com/Exabyte-io/api-examples/${GIT_BRANCH}/scripts/env.sh\" | bash\n",
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"\n",
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"if sys.platform == \"emscripten\":\n",
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" apiConfig = data_from_host.get(\"apiConfig\")\n",
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" os.environ.update(data_from_host.get(\"environ\", {}))\n",
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" os.environ.update(\n",
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" dict(\n",
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" ACCOUNT_ID=apiConfig.get(\"accountId\"),\n",
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" AUTH_TOKEN=apiConfig.get(\"authToken\"),\n",
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" ORGANIZATION_ID=apiConfig.get(\"organizationId\") or \"\",\n",
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" )\n",
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" )\n",
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"\n",
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"from mat3ra.notebooks_utils.packages import install_packages\n",
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"\n",
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"await install_packages(\"api\")"
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]
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},
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{
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"metadata": {},
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"cell_type": "code",
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"outputs": [],
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"metadata": {},
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"outputs": [],
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"source": [
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"from mat3ra.notebooks_utils.api.settings import ENDPOINT_ARGS, ACCOUNT_ID\n",
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"from mat3ra.notebooks_utils.ui import display_JSON\n",
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"from mat3ra.notebooks_utils.auth import authenticate\n",
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"\n",
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"from mat3ra.api_client.endpoints.jobs import JobEndpoints\n",
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"from mat3ra.api_client.endpoints.materials import MaterialEndpoints\n",
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"from mat3ra.api_client.endpoints.workflows import WorkflowEndpoints"
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"await authenticate()"
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {
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"id": "zjK-3ew_3sR7"
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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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"## Initialize the endpoints"
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"import os\n",
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"\n",
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"from mat3ra.api_client import APIClient\n",
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"\n",
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"client = APIClient.authenticate()\n",
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"selected_account = client.my_account\n",
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"OWNER_ID = os.getenv(\"ORGANIZATION_ID\") or selected_account.id"
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"metadata": {},
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"id": "IEPURdwU3sR7"
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},
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"outputs": [],
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"source": [
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"job_endpoints = JobEndpoints(*ENDPOINT_ARGS)\n",
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"material_endpoints = MaterialEndpoints(*ENDPOINT_ARGS)\n",
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"workflow_endpoints = WorkflowEndpoints(*ENDPOINT_ARGS)"
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"from mat3ra.notebooks_utils.ui import display_JSON"
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"Set job name."
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"source": "Set job name."
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"source": [
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"## Retrieve IDs\n",
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"\n",
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"Default account's materail and workflow are used in this example to create the job. Adjust the queries to use different material and workflow."
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"source": "## Retrieve IDs\n\nDefault account's materail and workflow are used in this example to create the job. Adjust the queries to use different material and workflow."
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"OWNER_ID = os.getenv(\"ORGANIZATION_ID\") or ACCOUNT_ID\n",
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"default_material = material_endpoints.list({\"isDefault\": True, \"owner._id\": OWNER_ID})[0]\n",
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"default_workflow = workflow_endpoints.list({\"isDefault\": True, \"owner._id\": OWNER_ID})[0]\n",
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"OWNER_ID = os.getenv(\"ORGANIZATION_ID\") or selected_account.id\n",
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"default_material = client.materials.list({\"isDefault\": True, \"owner._id\": OWNER_ID})[0]\n",
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"default_workflow = client.workflows.list({\"isDefault\": True, \"owner._id\": OWNER_ID})[0]\n",
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"material_id = default_material[\"_id\"]\n",
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"workflow_id = default_workflow[\"_id\"]"
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"source": [
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"## Create job config\n",
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"\n",
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"The job belongs to user's default account and it is created inside the defauult account's project. "
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"source": "## Create job config\n\nThe job belongs to user's default account and it is created inside the defauult account's project. "
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"source": [
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"## Create and submit job"
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"source": "## Create and submit job"
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"job = job_endpoints.create(config)\n",
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"job_endpoints.submit(job[\"_id\"])"
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"job = client.jobs.create(config)\n",
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"client.jobs.submit(job[\"_id\"])"
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"source": [
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"## Print the job\n",
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"\n",
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"source": "## Print the job\n\nPrint the job in pretty JSON below. Check `status` field to make sure job is submiited."
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"job = job_endpoints.get(job[\"_id\"])\n",
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"job = client.jobs.get(job[\"_id\"])\n",
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}

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