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VsevolodXVsevolodX
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update: swap mp to our bank
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‎examples/job/get-file-from-job.ipynb

+43-41
Original file line numberDiff line numberDiff line change
@@ -61,16 +61,13 @@
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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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"MATERIALS_PROJECT_API_KEY - Authentication parameter needed for when making requests to [Material Project's API](https://materialsproject.org/open)\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, MATERIALS_PROJECT_API_KEY, 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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},
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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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"cellView": "form",
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"colab": {
@@ -79,12 +76,12 @@
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"id": "nXDYU_oP8GIr",
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"outputId": "aee909b7-1a48-43c2-81b7-3659e0fc9c79"
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},
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"outputs": [],
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"source": [
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"from tokenize import blank_re\n",
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"\n",
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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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"MATERIALS_PROJECT_API_KEY = \"MATERIALS_PROJECT_API_KEY\" # @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",
@@ -95,7 +92,6 @@
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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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" MATERIALS_PROJECT_API_KEY=MATERIALS_PROJECT_API_KEY,\n",
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" ORGANIZATION_ID=ORGANIZATION_ID,\n",
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" )\n",
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" )\n",
@@ -109,7 +105,6 @@
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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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" MATERIALS_PROJECT_API_KEY=MATERIALS_PROJECT_API_KEY,\n",
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" ORGANIZATION_ID=apiConfig.get(\"organizationId\") or \"\",\n",
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" )\n",
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" )\n",
@@ -121,7 +116,9 @@
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" from utils.jupyterlite import install_packages\n",
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"\n",
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" await install_packages(\"\")"
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]
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],
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"outputs": [],
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"execution_count": null
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},
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{
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"attachments": {},
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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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"id": "rG9HfjnR8GIs"
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},
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"outputs": [],
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"source": [
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"# Import settings file and utils file\n",
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"from utils.settings import ENDPOINT_ARGS, ACCOUNT_ID, MATERIALS_PROJECT_API_KEY\n",
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"from utils.settings import ENDPOINT_ARGS, ACCOUNT_ID\n",
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"from utils.generic import (\n",
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" wait_for_jobs_to_finish,\n",
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" get_property_by_subworkflow_and_unit_indicies,\n",
@@ -154,9 +149,11 @@
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"from exabyte_api_client.endpoints.jobs import JobEndpoints\n",
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"from exabyte_api_client.endpoints.projects import ProjectEndpoints\n",
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"from exabyte_api_client.endpoints.materials import MaterialEndpoints\n",
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"from exabyte_api_client.endpoints.bank_workflows import BankWorkflowEndpoints\n",
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"from exabyte_api_client.endpoints.properties import PropertiesEndpoints"
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]
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"from exabyte_api_client.endpoints.bank_materials import BankMaterialEndpoints\n",
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"from exabyte_api_client.endpoints.bank_workflows import BankWorkflowEndpoints"
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],
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"outputs": [],
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"execution_count": null
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},
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{
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"attachments": {},
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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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"colab": {
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"base_uri": "https://localhost:8080/"
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},
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"id": "le9f28c08GIt",
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"outputId": "27e9b94f-29dd-4742-9448-2e1bce79cb15"
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},
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"outputs": [],
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"source": [
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"# Get some account information\n",
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"project_endpoints = ProjectEndpoints(*ENDPOINT_ARGS)\n",
@@ -199,13 +194,18 @@
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"\n",
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"# Get a workflow for the job from the bank, and copy it to our account\n",
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"bank_workflow_endpoints = BankWorkflowEndpoints(*ENDPOINT_ARGS)\n",
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"BANK_WORKFLOW_ID = \"84DAjE9YyTFndx6z3\"\n",
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"workflow_id = bank_workflow_endpoints.copy(BANK_WORKFLOW_ID, owner_id)[\"_id\"]\n",
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"\n",
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"# Get materials for the job\n",
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"WORKFLOW_QUERY = {\"systemName\": \"espresso-total-energy\"}\n",
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"bank_workflow_id = bank_workflow_endpoints.list(WORKFLOW_QUERY)[0][\"_id\"]\n",
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"workflow_id = bank_workflow_endpoints.copy(bank_workflow_id, owner_id)[\"_id\"]\n",
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"\n",
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"# Get materials from bank and copy one to our account\n",
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"material_bank_endpoints = BankMaterialEndpoints(*ENDPOINT_ARGS)\n",
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"MATERIAL_QUERY = {\"formula\": \"Si\"}\n",
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"bank_materials = material_bank_endpoints.list(MATERIAL_QUERY)\n",
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"bank_material_id = bank_materials[0][\"_id\"]\n",
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"material_endpoints = MaterialEndpoints(*ENDPOINT_ARGS)\n",
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"material_project_id = [\"mp-149\"] # The importer expects a list\n",
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"materials = material_endpoints.import_from_materialsproject(MATERIALS_PROJECT_API_KEY, material_project_id, owner_id)\n",
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"material_id = material_bank_endpoints.copy(bank_material_id, owner_id)[\"_id\"]\n",
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"materials = material_endpoints.list({\"owner._id\": owner_id})\n",
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"\n",
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"# Create the job\n",
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"job_endpoints = JobEndpoints(*ENDPOINT_ARGS)\n",
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"# Submit the job\n",
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"job_endpoints.submit(job[\"_id\"])\n",
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"wait_for_jobs_to_finish(job_endpoints, [job[\"_id\"]])"
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]
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],
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"outputs": [],
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"execution_count": null
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},
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{
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"attachments": {},
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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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"colab": {
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"base_uri": "https://localhost:8080/"
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},
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"id": "yijRe7qp8GIv",
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"outputId": "19b147fc-736e-41f0-bd0f-6f69e77b0adf"
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},
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"outputs": [],
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"source": [
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"files = job_endpoints.list_files(job[\"_id\"])\n",
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"paths = [file[\"key\"] for file in files]\n",
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"for path in paths:\n",
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" if \"outdir\" not in path:\n",
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" print(path)"
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]
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],
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"outputs": [],
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"execution_count": null
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},
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{
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"attachments": {},
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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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"colab": {
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"base_uri": "https://localhost:8080/"
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},
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"id": "U2dq0A1e8GIw",
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"outputId": "7b4f8c36-6342-46fa-d02e-0825b44e6c64"
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},
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"outputs": [],
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"source": [
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"for file in files:\n",
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" if file[\"name\"] == \"pw_scf.out\":\n",
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" output_file_metadata = file\n",
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"display_JSON(output_file_metadata)"
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]
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],
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"outputs": [],
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"execution_count": null
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},
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{
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"attachments": {},
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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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"colab": {
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"base_uri": "https://localhost:8080/"
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},
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"id": "OpdOMuDT8GIw",
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"outputId": "e4e2e6b1-8431-439a-8606-ae500534e601"
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},
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"outputs": [],
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"source": [
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"import urllib\n",
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"\n",
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"lines = output_file.split(\"\\n\")\n",
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"for line in lines[-90:]:\n",
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" print(line)"
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]
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],
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"outputs": [],
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"execution_count": null
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},
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{
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"attachments": {},
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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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"id": "osy2JKpB8GIx"
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},
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"outputs": [],
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"source": [
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"# We've already got an output file, so let's grab the input file we sent to Quantum Espresso\n",
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"for file in files:\n",
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" if \"pw_scf.in\" == file[\"name\"]:\n",
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" input_file_metadata = file\n",
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"server_response = urllib.request.urlopen(input_file_metadata[\"signedUrl\"])\n",
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"input_file_bytes = server_response.read()"
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]
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],
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"outputs": [],
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"execution_count": null
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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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"id": "COPinBrO8GIx"
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},
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"outputs": [],
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"source": [
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"# Let's write the input file to disk. Note that we get files as a bytes string from the server, which is convenient for binaries, images, and other non-human-readable data.\n",
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"# Although we could decode before writing to disk, we can just write it directly with the \"wb\" (write bytes) file mode.\n",
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"with open(input_file_metadata[\"name\"], \"wb\") as file_descriptor:\n",
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" file_descriptor.write(input_file_bytes)"
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]
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],
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"outputs": [],
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"execution_count": null
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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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"id": "rzDcWyrL8GIx"
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},
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"outputs": [],
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"source": [
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"# Now, let's write our output file to the disk. Note that because we already decoded it, we can just use the 'w' file mode.\n",
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"with open(output_file_metadata[\"name\"], \"w\") as file_descriptor:\n",
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" file_descriptor.write(output_file)"
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]
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],
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"outputs": [],
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"execution_count": null
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}
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],
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"metadata": {

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