update

README.md

@@ -2,6 +2,8 @@
 
 `git clone --recurse-submodules https://gitlab.liris.cnrs.fr/sharefair/bioflow-insight-study.git`
 
+`git submodule update --recursive --remote`
+
 tets
 ## Getting started
 

github-crawler @ bf632200

-Subproject commit 537540936dd0a3fc07e5f0143d74fa7cf93735bb
+Subproject commit bf6322002948c7b3df3657e0bd0e5fd82e7c8bd5

study.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import json"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from github_crawler.download_corpus import"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "* 1/752\n",
+      "Downloading...'HadrienG/nextflow_rna'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/HadrienG/nextflow_rna'...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "\n",
+      "* 2/752\n",
+      "Downloading...'IARCbioinfo/CODEX-nf'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/IARCbioinfo/CODEX-nf'...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "\n",
+      "* 3/752\n",
+      "Downloading...'AndersenLab/ril-nf'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/AndersenLab/ril-nf'...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "\n",
+      "* 4/752\n",
+      "Downloading...'robsyme/markerdev'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/robsyme/markerdev'...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "\n",
+      "* 5/752\n",
+      "\n",
+      "\n",
+      "\n",
+      "* 6/752\n",
+      "Downloading...'ctmrbio/BACTpipe'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/ctmrbio/BACTpipe'...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "\n",
+      "* 7/752\n",
+      "Downloading...'danielecook/nextflow-tutorial'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/danielecook/nextflow-tutorial'...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "\n",
+      "* 8/752\n",
+      "Downloading...'IARCbioinfo/bamsurgeon-nf'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/IARCbioinfo/bamsurgeon-nf'...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "\n",
+      "* 9/752\n",
+      "Downloading...'nextflow-io/cwl2nxf'\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "mkdir: opérande manquant\n",
+      "Saisissez « mkdir --help » pour plus d'informations.\n",
+      "Clonage dans '../../../Workflow-Corpus-Open-License/nextflow-io/cwl2nxf'...\n"
+     ]
+    }
+   ],
+   "source": [
+    "\n",
+    "current_path= os.getcwd()\n",
+    "os.chdir(\"github-crawler/\")\n",
+    "from download_corpus import *\n",
+    "os.chdir(current_path)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "download_files = True\n",
+    "repo_to_download = \"../Workflow-Corpus-Open-Licence/\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#Read crawler results\n",
+    "with open(\"./github-crawler/wf_crawl_nextflow.json\") as json_file:\n",
+    "    crawler = json.load(json_file)\n",
+    "\n",
+    "_ = crawler.pop(\"last_date\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if(download_files):\n",
+    "    current_directory = os.getcwd()\n",
+    "    os.chdir(current_directory+'/'+repo_to_download)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/home/gmarchment/Documents/These/Work/Workflow-Corpus-Open-Licence'"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "os.getcwd()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}