From 7490d6f648e011fd22715004169f4cf48a55bfbf Mon Sep 17 00:00:00 2001
From: Jasper Koehorst <jasper.koehorst@wur.nl>
Date: Tue, 30 Mar 2021 18:07:05 +0200
Subject: [PATCH] kraken prepare and local endpoint loader added. biom rmd
updates
---
notebooks/SPARQLEndpointLoader.ipynb | 381 +++++++++++++++++++++++++++
notebooks/amplicon-biom.Rmd | 2 +-
notebooks/kraken-biom.Rmd | 2 +-
notebooks/kraken-prepare.ipynb | 222 ++++++++++++++++
4 files changed, 605 insertions(+), 2 deletions(-)
create mode 100644 notebooks/SPARQLEndpointLoader.ipynb
create mode 100644 notebooks/kraken-prepare.ipynb
diff --git a/notebooks/SPARQLEndpointLoader.ipynb b/notebooks/SPARQLEndpointLoader.ipynb
new file mode 100644
index 0000000..8201e9a
--- /dev/null
+++ b/notebooks/SPARQLEndpointLoader.ipynb
@@ -0,0 +1,381 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# SPARQL Endpoint loader"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Username\n"
+ ]
+ },
+ {
+ "name": "stdin",
+ "output_type": "stream",
+ "text": [
+ " koehorst\n"
+ ]
+ }
+ ],
+ "source": [
+ "import getpass\n",
+ "print(\"Username\")\n",
+ "username=input()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Password\n"
+ ]
+ },
+ {
+ "name": "stdin",
+ "output_type": "stream",
+ "text": [
+ " ··············\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(\"Password\")\n",
+ "password = getpass.getpass()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### SPARQL database functions"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 88,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def create_sparql_config(repo):\n",
+ " turtle = \"\"\"\n",
+ " # RDF4J configuration template for a GraphDB Free repository\n",
+ "\n",
+ " @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n",
+ " @prefix rep: <http://www.openrdf.org/config/repository#>.\n",
+ " @prefix sr: <http://www.openrdf.org/config/repository/sail#>.\n",
+ " @prefix sail: <http://www.openrdf.org/config/sail#>.\n",
+ " @prefix owlim: <http://www.ontotext.com/trree/owlim#>.\n",
+ "\n",
+ " [] a rep:Repository ;\n",
+ " rep:repositoryID \\\"\"\"\"+repo+\"\"\"\\\" ;\n",
+ " rdfs:label \"GraphDB Free repository\" ;\n",
+ " rep:repositoryImpl [\n",
+ " rep:repositoryType \"graphdb:FreeSailRepository\" ;\n",
+ " sr:sailImpl [\n",
+ " sail:sailType \"graphdb:FreeSail\" ;\n",
+ "\n",
+ " owlim:base-URL \"http://gbol.life/0.1/\" ;\n",
+ " owlim:defaultNS \"\" ;\n",
+ " owlim:entity-index-size \"10000000\" ;\n",
+ " owlim:entity-id-size \"32\" ;\n",
+ " owlim:imports \"\" ;\n",
+ " owlim:repository-type \"file-repository\" ;\n",
+ " owlim:ruleset \"rdfsplus-optimized\" ;\n",
+ " owlim:storage-folder \"storage\" ;\n",
+ "\n",
+ " owlim:enable-context-index \"false\" ;\n",
+ "\n",
+ " owlim:enablePredicateList \"true\" ;\n",
+ "\n",
+ " owlim:in-memory-literal-properties \"true\" ;\n",
+ " owlim:enable-literal-index \"true\" ;\n",
+ "\n",
+ " owlim:check-for-inconsistencies \"false\" ;\n",
+ " owlim:disable-sameAs \"false\" ;\n",
+ " owlim:query-timeout \"0\" ;\n",
+ " owlim:query-limit-results \"0\" ;\n",
+ " owlim:throw-QueryEvaluationException-on-timeout \"false\" ;\n",
+ " owlim:read-only \"false\" ;\n",
+ " owlim:nonInterpretablePredicates \"http://www.w3.org/2000/01/rdf-schema#label;http://www.w3.org/1999/02/22-rdf-syntax-ns#type;http://www.ontotext.com/owlim/ces#gazetteerConfig;http://www.ontotext.com/owlim/ces#metadataConfig\" ;\n",
+ " ]\n",
+ " ].\n",
+ " \"\"\"\n",
+ "\n",
+ " open(repo + \"_config.ttl\", \"w\").write(turtle)\n",
+ " logger.info(\"Config file created\")\n",
+ "\n",
+ "\n",
+ "def curl(repo, filename):\n",
+ " url = 'http://graphdb:7200/repositories/' + repo + \"/statements\"\n",
+ " payload = open(filename,'rb').read()\n",
+ " headers = {'content-type': 'text/turtle'}\n",
+ " index = 0\n",
+ " while True:\n",
+ " index = index + 1\n",
+ " r = requests.post(url, data=payload, headers=headers, auth=HTTPBasicAuth(username, password), timeout=1000)\n",
+ " if int(r.status_code) == 200:\n",
+ " return True\n",
+ " if int(r.status_code) == 204:\n",
+ " # TODO\n",
+ " return True\n",
+ " if index > 2:\n",
+ " return r\n",
+ " if int(r.status_code) == 502:\n",
+ " return r\n",
+ "# if int(r.status_code) == 404:\n",
+ "# return r\n",
+ " print(\"Request post failed... exit code \",r.status_code,\" retrying \", index)\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### iRODS dependencies \n",
+ "These dependencies are needed if not supplied from the docker file"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 89,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pathlib\n",
+ "# RDF Insertion\n",
+ "from SPARQLWrapper import SPARQLWrapper, JSON\n",
+ "# iRODS\n",
+ "from irods.session import iRODSSession\n",
+ "from irods.column import Criterion\n",
+ "from irods.models import DataObject, DataObjectMeta, Collection, CollectionMeta\n",
+ "from irods.session import iRODSSession\n",
+ "# Python\n",
+ "import os\n",
+ "import shutil\n",
+ "# Logging\n",
+ "import logging\n",
+ "# Authentication curl\n",
+ "import requests\n",
+ "from requests.auth import HTTPBasicAuth\n",
+ "\n",
+ "LOGGING_FORMAT = '[%(asctime)-15s][%(levelname)-7s] %(message)s'\n",
+ "\n",
+ "def get_logger(name):\n",
+ " logging.basicConfig(format=LOGGING_FORMAT)\n",
+ " logger = logging.getLogger(name)\n",
+ " logger.setLevel('DEBUG')\n",
+ " return logger\n",
+ "\n",
+ "logger = get_logger(\"jupyter\")\n",
+ "# Configurations\n",
+ "%config IPCompleter.greedy=True"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### iRODS connection"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 90,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "[2021-03-29 15:25:11,346][INFO ] <iRODSCollection 10005 b'unlock'>\n"
+ ]
+ }
+ ],
+ "source": [
+ "from irods.session import iRODSSession\n",
+ "import ssl\n",
+ "\n",
+ "# iRODS authentication information\n",
+ "host = \"unlock-icat.irods.surfsara.nl\"\n",
+ "port = \"1247\"\n",
+ "zone = \"unlock\"\n",
+ "\n",
+ "context = ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH, cafile=None, capath=None, cadata=None)\n",
+ "\n",
+ "ssl_settings = {'irods_client_server_negotiation': 'request_server_negotiation',\n",
+ " 'irods_client_server_policy': 'CS_NEG_REQUIRE',\n",
+ " 'irods_encryption_algorithm': 'AES-256-CBC',\n",
+ " 'irods_encryption_key_size': 32,\n",
+ " 'irods_encryption_num_hash_rounds': 16,\n",
+ " 'irods_encryption_salt_size': 8,\n",
+ " 'ssl_context': context}\n",
+ "\n",
+ "\n",
+ "session = iRODSSession(host = host,\n",
+ " port = port,\n",
+ " user = username,\n",
+ " password = password,\n",
+ " zone = zone,\n",
+ " **ssl_settings)\n",
+ "\n",
+ "coll = session.collections.get('/unlock')\n",
+ "logger.info(coll)\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### List projects with access\n",
+ "This section lists all projects the current user has access to. This can be used to set the `IDENTIFIER` to the right project."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 91,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "[2021-03-29 15:25:11,386][INFO ] P_Deltares\n",
+ "[2021-03-29 15:25:11,407][INFO ] P_Deltares/I_vitens\n",
+ "[2021-03-29 15:25:11,408][INFO ] P_E2BN\n",
+ "[2021-03-29 15:25:11,424][INFO ] P_E2BN/I_PRED\n",
+ "[2021-03-29 15:25:11,425][INFO ] P_EXPLODIV\n",
+ "[2021-03-29 15:25:11,447][INFO ] P_EXPLODIV/I_BIOGAS\n",
+ "[2021-03-29 15:25:11,448][INFO ] P_EXPLODIV/I_UNCOUPLED\n",
+ "[2021-03-29 15:25:11,448][INFO ] P_FIRM-Project\n",
+ "[2021-03-29 15:25:11,467][INFO ] P_FIRM-Project/I_FIRM-Broilers\n",
+ "[2021-03-29 15:25:11,468][INFO ] P_MIB-Amplicon\n",
+ "[2021-03-29 15:25:11,484][INFO ] P_MIB-Amplicon/I_Mocks\n",
+ "[2021-03-29 15:25:11,485][INFO ] P_MIB-Amplicon/I_Poultry_16S_MIB\n",
+ "[2021-03-29 15:25:11,485][INFO ] P_SIAM\n",
+ "[2021-03-29 15:25:11,505][INFO ] P_SIAM/I_DbMM\n",
+ "[2021-03-29 15:25:11,506][INFO ] P_UNLOCK\n",
+ "[2021-03-29 15:25:11,528][INFO ] P_UNLOCK/I_CAMI\n",
+ "[2021-03-29 15:25:11,529][INFO ] P_UNLOCK/I_INVESTIGATION_TEST\n",
+ "[2021-03-29 15:25:11,530][INFO ] P_UNLOCK/I_SRA_Amplicon\n"
+ ]
+ }
+ ],
+ "source": [
+ "projects = session.collections.get(\"/unlock/projects\").subcollections\n",
+ "for project in projects:\n",
+ " logger.info(project.name)\n",
+ " for investigation in project.subcollections:\n",
+ " if investigation.name.startswith(\"I_\"):\n",
+ " logger.info(project.name + \"/\" + investigation.name)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Downloading metadata rdf files"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 92,
+ "metadata": {
+ "scrolled": true,
+ "tags": []
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "[2021-03-29 15:25:11,666][INFO ] P_Deltares\n",
+ "[2021-03-29 15:25:12,294][INFO ] Config file created\n",
+ "[2021-03-29 15:25:13,300][INFO ] P_E2BN\n",
+ "[2021-03-29 15:25:15,387][INFO ] Config file created\n",
+ "[2021-03-29 15:25:49,299][INFO ] P_EXPLODIV\n",
+ "[2021-03-29 15:25:49,341][INFO ] P_FIRM-Project\n",
+ "[2021-03-29 15:25:49,372][INFO ] P_MIB-Amplicon\n",
+ "[2021-03-29 15:25:50,038][INFO ] Config file created\n",
+ "[2021-03-29 15:26:02,140][INFO ] Config file created\n",
+ "[2021-03-29 15:26:56,839][INFO ] Config file created\n",
+ "[2021-03-29 15:26:58,794][INFO ] P_SIAM\n",
+ "[2021-03-29 15:26:58,832][INFO ] P_UNLOCK\n",
+ "[2021-03-29 15:26:59,083][INFO ] Config file created\n",
+ "[2021-03-29 15:27:02,962][INFO ] Config file created\n"
+ ]
+ }
+ ],
+ "source": [
+ "projects = session.collections.get(\"/unlock/projects\").subcollections\n",
+ "for project in projects:\n",
+ " logger.info(project.name)\n",
+ " for investigation in project.subcollections:\n",
+ " if investigation.name.startswith(\"I_\"):\n",
+ " for obj in investigation.data_objects:\n",
+ " if obj.name.endswith(\".ttl\"):\n",
+ " if obj.name.startswith(\".\"): continue\n",
+ " local_path = \"./data/\" + investigation.path\n",
+ " destination = local_path + \"/\" + obj.name\n",
+ " os.makedirs(local_path, exist_ok=True)\n",
+ " options = {kw.FORCE_FLAG_KW:\"\"}\n",
+ " session.data_objects.get(obj.path, destination, **options)\n",
+ " endpoint_name = project.name + \"_\" + investigation.name\n",
+ " create_sparql_config(endpoint_name)\n",
+ " # Execute config file to create repository\n",
+ " command = \"curl -X POST graphdb:7200/rest/repositories -H 'Accept: application/json' -H 'Content-Type: multipart/form-data' -F config=@\"+endpoint_name+\"_config.ttl\"\n",
+ " os.system(command)\n",
+ " # Load files\n",
+ " curl(endpoint_name, destination)\n"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.8"
+ },
+ "toc": {
+ "base_numbering": 1,
+ "nav_menu": {},
+ "number_sections": false,
+ "sideBar": false,
+ "skip_h1_title": false,
+ "title_cell": "Table of Contents",
+ "title_sidebar": "Contents",
+ "toc_cell": false,
+ "toc_position": {},
+ "toc_section_display": false,
+ "toc_window_display": false
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/notebooks/amplicon-biom.Rmd b/notebooks/amplicon-biom.Rmd
index 3790f41..47defc3 100644
--- a/notebooks/amplicon-biom.Rmd
+++ b/notebooks/amplicon-biom.Rmd
@@ -52,7 +52,7 @@ WHERE {
?ISAsample unlock:assay ?assay .
?assay schema:identifier ?id .
}"
-results = SPARQL(url = "http://172.18.0.2:7200/repositories/P_E2BN_I_PRED", format = "csv", query = query)$results
+results = SPARQL(url = "http://graphdb:7200/repositories/P_E2BN_I_PRED", format = "csv", query = query)$results
results$predicate = gsub(x = results$predicate, pattern = ".*/", replacement = "")
metadata <- dcast(results, id ~ predicate, value.var = "object")
rownames(metadata) = metadata$id
diff --git a/notebooks/kraken-biom.Rmd b/notebooks/kraken-biom.Rmd
index 8c7a422..fc2d0bd 100644
--- a/notebooks/kraken-biom.Rmd
+++ b/notebooks/kraken-biom.Rmd
@@ -21,7 +21,7 @@ The preview shows you a rendered HTML copy of the contents of the editor. Conseq
```{r}
# Load Kraken json object generated from jupyter hub
-physeq = import_biom("data/P_Deltares-I_vitens_kraken.json")
+physeq = import_biom("data/unlock/projects/P_Deltares/I_vitens/kraken.json")
# Fix rank naming issue from kraken data
colnames(tax_table(physeq)) = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
# Correct input names
diff --git a/notebooks/kraken-prepare.ipynb b/notebooks/kraken-prepare.ipynb
new file mode 100644
index 0000000..177bd3a
--- /dev/null
+++ b/notebooks/kraken-prepare.ipynb
@@ -0,0 +1,222 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "typical-perfume",
+ "metadata": {},
+ "source": [
+ "# Generate kraken biom files"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "bridal-niger",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Install kraken-biom package\n",
+ "!pip install kraken-biom"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "pharmaceutical-pattern",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Dependencies\n",
+ "import os\n",
+ "import logging\n",
+ "from irods.models import DataObject, DataObjectMeta, Collection, CollectionMeta\n",
+ "from irods.column import Criterion\n",
+ "import getpass\n",
+ "from shutil import copyfileobj\n",
+ "import pathlib\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "right-allocation",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Generic functions\n",
+ "LOGGING_FORMAT = '[%(asctime)-15s][%(levelname)-7s] %(message)s'\n",
+ "\n",
+ "def get_logger(name):\n",
+ " logging.basicConfig(format=LOGGING_FORMAT)\n",
+ " logger = logging.getLogger(name)\n",
+ " logger.setLevel('DEBUG')\n",
+ " return logger\n",
+ "\n",
+ "logger = get_logger(\"jupyter\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "minor-square",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "## iRODS authentication"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "recognized-camcorder",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "print(\"Username\")\n",
+ "username=input()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "designed-surveillance",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "print(\"Password\")\n",
+ "password = getpass.getpass()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "flexible-sunglasses",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from irods.session import iRODSSession\n",
+ "import ssl\n",
+ "\n",
+ "# iRODS authentication information\n",
+ "host = \"unlock-icat.irods.surfsara.nl\"\n",
+ "port = \"1247\"\n",
+ "zone = \"unlock\"\n",
+ "\n",
+ "context = ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH, cafile=None, capath=None, cadata=None)\n",
+ "\n",
+ "ssl_settings = {'irods_client_server_negotiation': 'request_server_negotiation',\n",
+ " 'irods_client_server_policy': 'CS_NEG_REQUIRE',\n",
+ " 'irods_encryption_algorithm': 'AES-256-CBC',\n",
+ " 'irods_encryption_key_size': 32,\n",
+ " 'irods_encryption_num_hash_rounds': 16,\n",
+ " 'irods_encryption_salt_size': 8,\n",
+ " 'ssl_context': context}\n",
+ "\n",
+ "\n",
+ "session = iRODSSession(host = host,\n",
+ " port = port,\n",
+ " user = username,\n",
+ " password = password,\n",
+ " zone = zone,\n",
+ " **ssl_settings)\n",
+ "\n",
+ "projects = session.collections.get(\"/unlock/projects\").subcollections\n",
+ "for project in projects:\n",
+ " for investigation in project.subcollections:\n",
+ " if investigation.name.startswith(\"I_\"):\n",
+ " logger.info(\"Access to project: \" + project.name + \" and investigation \" + investigation.name)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "surrounded-assurance",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Obtain all kraken files for a given project and investigation\n",
+ "# project = \"P_Deltares\"\n",
+ "# investigation = \"I_vitens\"\n",
+ "for project in projects:\n",
+ " for investigation in project.subcollections:\n",
+ " if investigation.name.startswith(\"I_\"):\n",
+ " logger.info(\"Access to project: \" + project.name + \" and investigation \" + investigation.name)\n",
+ " \n",
+ " results = session.query(Collection, DataObject).filter( \\\n",
+ " Criterion('like', DataObject.path,\"%_kraken2_report.txt\")).filter( \\\n",
+ " Criterion('like', Collection.name, investigation.path + \"/%\"))\n",
+ "\n",
+ " file_paths = set()\n",
+ "\n",
+ " # Obtaining all files\n",
+ " logger.info(\"Collecting all paths\")\n",
+ " index = 0\n",
+ " for index, r in enumerate(results):\n",
+ " file_path = r.get(Collection.name) + \"/\" + r.get(DataObject.name)\n",
+ " obj = session.data_objects.get(file_path)\n",
+ " output_dir = './data' + r.get(Collection.name)\n",
+ " pathlib.Path(output_dir).mkdir(parents=True, exist_ok=True)\n",
+ " output_file = './data' + file_path\n",
+ " file_paths.add(output_file)\n",
+ " if os.path.isfile(output_file): continue\n",
+ " with open(output_file, 'wb') as output, obj.open('r+') as input:\n",
+ " copyfileobj(input, output)\n",
+ "\n",
+ " # Skipp projects with no kraken files\n",
+ " if index == 0: continue\n",
+ " \n",
+ " logger.info(\"Obtained \" + str(index) + \" kraken files\")\n",
+ " \n",
+ " # Creating biom file from kraken reports\n",
+ " command = \"kraken-biom \" + ' '.join(file_paths) + \" --fmt json -o ./data/\" + investigation.path + \"/kraken.json\"\n",
+ " logger.info(\"Command: \" + command)\n",
+ " os.system(command)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "comic-parker",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "corporate-knowing",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "matched-parallel",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
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+ "pygments_lexer": "ipython3",
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+ }
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+ "nbformat": 4,
+ "nbformat_minor": 5
+}
--
GitLab