{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# !pip install datasets[s3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import datasets\n",
    "import json\n",
    "from datasets import load_from_disk\n",
    "\n",
    "s3 = datasets.filesystems.S3FileSystem(anon=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# GTEx"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "s3 = datasets.filesystems.S3FileSystem(anon=True) \n",
    "gtex_code2tissue = {}\n",
    "gtex_tissue2filepath = {}\n",
    "\n",
    "PATH = \"recount-opendata/recount3/release/human/data_sources/gtex/gene_sums/\"\n",
    "\n",
    "for dirpath, dirnames, filenames in s3.walk(PATH):\n",
    "# care about the how many directories your bucket have\n",
    "    dirpath_ = dirpath.split('/')\n",
    "    if len(dirpath_) == 9:\n",
    "        gtex_code2tissue[dirpath_[-2]] = dirpath_[-1]\n",
    "        for filename in filenames:\n",
    "            if \"G029\" in filename:\n",
    "                file_path = os.path.join(dirpath, filename)\n",
    "                gtex_tissue2filepath[dirpath_[-1]] = file_path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# gtex_tissue2filepath\n",
    "# gtex_code2tissue\n",
    "\n",
    "for filename, d in {\n",
    "    \"gtex_tissue2filepath.json\": gtex_tissue2filepath,\n",
    "    \"gtex_code2tissue.json\": gtex_code2tissue,\n",
    "}.items():\n",
    "    js_dump = json.dumps(d, sort_keys=True, indent=4, separators=(',', \": \"))\n",
    "    with open(filename, 'w+') as f:\n",
    "        f.write(js_dump)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# TCGA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "s3 = datasets.filesystems.S3FileSystem(anon=True) \n",
    "tcga_code2cancer = {}\n",
    "tcga_cancer2filepath = {}\n",
    "for dirpath, dirnames, filenames in s3.walk(\"recount-opendata/recount3/release/human/data_sources/tcga/gene_sums/\"):\n",
    "# care about the how many directories your bucket have\n",
    "    dirpath_ = dirpath.split('/')\n",
    "    if len(dirpath_) == 9:\n",
    "        tcga_code2cancer[dirpath_[-2]] = dirpath_[-1]\n",
    "        for filename in filenames:\n",
    "            if \"G029\" in filename:\n",
    "                file_path = os.path.join(dirpath, filename)\n",
    "                tcga_cancer2filepath[dirpath_[-1]] = file_path\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# tcga_cancer2filepath\n",
    "# tcga_code2cancer\n",
    "\n",
    "for filename, d in {\n",
    "    \"tcga_cancer2filepath.json\": tcga_cancer2filepath,\n",
    "    \"tcga_code2cancer.json\": tcga_code2cancer,\n",
    "}.items():\n",
    "    js_dump = json.dumps(d, sort_keys=True, indent=4, separators=(',', \": \"))\n",
    "    with open(filename, 'w+') as f:\n",
    "        f.write(js_dump)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# SRA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "s3 = datasets.filesystems.S3FileSystem(anon=True) \n",
    "sra_dir2studies = {}\n",
    "sra_study2filepath = {}\n",
    "for dirpath, dirnames, filenames in s3.walk(\"recount-opendata/recount3/release/human/data_sources/sra/gene_sums/\"):\n",
    "# care about the how many directories your bucket have\n",
    "    dirpath_ = dirpath.split('/')\n",
    "    if len(dirpath_) == 9:\n",
    "        if dirpath_[-2] in sra_dir2studies:\n",
    "            sra_dir2studies[dirpath_[-2]].append(dirpath_[-1])\n",
    "        else:\n",
    "            sra_dir2studies[dirpath_[-2]] = [dirpath_[-1]]\n",
    "            \n",
    "        for filename in filenames:\n",
    "            if \"G029\" in filename:\n",
    "                file_path = os.path.join(dirpath, filename)\n",
    "                sra_study2filepath[dirpath_[-1]] = file_path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "for filename, d in {\n",
    "    \"sra_study2filepath.json\": sra_study2filepath,\n",
    "    \"sra_dir2studies.json\": sra_dir2studies,\n",
    "}.items():\n",
    "    js_dump = json.dumps(d, sort_keys=True, indent=4, separators=(',', \": \"))\n",
    "    with open(filename, 'w+') as f:\n",
    "        f.write(js_dump)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# s3.ls(\"recount-opendata/recount3/release/human/data_sources/sra/gene_sums/00/DRP003300\")"
   ]
  }
 ],
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