From 04cc51945b9e685ae771e2e2340437541fd050f4 Mon Sep 17 00:00:00 2001 From: Ekaterina Sakharova Date: Wed, 10 Apr 2024 11:14:15 +0100 Subject: [PATCH] fixes after review --- .../Atlanteco Interactive Sample Map.ipynb | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/src/notebooks/Python Examples/Atlanteco Interactive Sample Map.ipynb b/src/notebooks/Python Examples/Atlanteco Interactive Sample Map.ipynb index d10e415..1f71475 100644 --- a/src/notebooks/Python Examples/Atlanteco Interactive Sample Map.ipynb +++ b/src/notebooks/Python Examples/Atlanteco Interactive Sample Map.ipynb @@ -12,8 +12,7 @@ "author: \"Kate S [Ekaterina Sakharova] (MGnify team)\"\n", "categories: [Python]\n", "execute: \n", - " enabled: false\n", - " eval: false\n", + " eval: true\n", "---" ] }, @@ -274,22 +273,26 @@ "We can fetch the Samples for each Study, and concatenate them all into one Dataframe.\n", "Each sample has geolocation data in its `attributes` - this is what we need to build a map.\n", "\n", - "It takes time to fetch data for all samples, so **let's show samples from chosen PRJEB46727 study only.** This study contain assembly data https://www.ebi.ac.uk/metagenomics/studies/MGYS00005810#overview." + "It takes time to fetch data for all samples, so **let's show samples from chosen PRJEB46727 study only.** This study contains assembly data https://www.ebi.ac.uk/metagenomics/studies/MGYS00005810#overview." ] }, { "cell_type": "code", - "execution_count": 266, + "execution_count": 1, "id": "bc5d0fc9-5c05-4bb1-b401-507b6e8c8877", "metadata": { "tags": [] }, "outputs": [ { - "name": "stdout", - "output_type": "stream", - "text": [ - "fetching MGYS00005810 samples\n" + "ename": "NameError", + "evalue": "name 'studies' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m substudy \u001b[38;5;241m=\u001b[39m \u001b[43mstudies\u001b[49m[studies[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mattributes.bioproject\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPRJEB46727\u001b[39m\u001b[38;5;124m'\u001b[39m]\n\u001b[1;32m 2\u001b[0m studies_samples \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m Session(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mhttps://www.ebi.ac.uk/metagenomics/api/v1\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01mas\u001b[39;00m mgnify:\n", + "\u001b[0;31mNameError\u001b[0m: name 'studies' is not defined" ] } ],