update galaxy.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# update_history 4792"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from bioblend import galaxy\n",
    "\n",
    "gi = galaxy.GalaxyInstance(url='https://usegalaxy.eu', key='')\n",
    "\n",
    "hl = gi.histories.get_histories()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "hl = gi.histories.get_histories()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "107"
      ]
     },
     "execution_count": 55,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(hl)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'name': 'diploids', 'tags': [], 'deleted': False, 'purged': False, 'annotation': None, 'url': '/api/histories/020f877513f2d0d1', 'published': False, 'model_class': 'History', 'id': '020f877513f2d0d1'}\n"
     ]
    }
   ],
   "source": [
    "for x in hl:\n",
    "    if 'diploids' in x['name']:\n",
    "        print(x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "foo = gi.histories.show_history('020f877513f2d0d1',contents=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-21T08:55:01.497214',\n",
       "  'name': 'Pasted Entry',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a59310d3c5b067c05',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a59310d3c5b067c05',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T08:50:20.858625',\n",
       "  'hid': 1,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a59310d3c5b067c05',\n",
       "  'dataset_id': '8f4505676d972a27',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590687',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/003/SRR1658693/SRR1658693_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33ac470b9be95baf60c',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33ac470b9be95baf60c',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:07.441510',\n",
       "  'hid': 2,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33ac470b9be95baf60c',\n",
       "  'dataset_id': '8850f389d8ca7116',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590707',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/003/SRR1658693/SRR1658693_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aba786faa9feb651a',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aba786faa9feb651a',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.074746',\n",
       "  'hid': 3,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aba786faa9feb651a',\n",
       "  'dataset_id': 'de2bae9096af265b',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590721',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/004/SRR1658694/SRR1658694_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33ade8470111b6ba81d',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33ade8470111b6ba81d',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.177966',\n",
       "  'hid': 4,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33ade8470111b6ba81d',\n",
       "  'dataset_id': '5e979e5c983252eb',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590730',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/004/SRR1658694/SRR1658694_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aa0b4a90b2ce019a1',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aa0b4a90b2ce019a1',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.257474',\n",
       "  'hid': 5,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aa0b4a90b2ce019a1',\n",
       "  'dataset_id': '4ae5b7dd9de03229',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590737',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/005/SRR1658695/SRR1658695_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a6e17802ee4601af9',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a6e17802ee4601af9',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.337909',\n",
       "  'hid': 6,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a6e17802ee4601af9',\n",
       "  'dataset_id': 'bbca042d2c0c25b3',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590749',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/005/SRR1658695/SRR1658695_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a8d26acedf31aa4ab',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a8d26acedf31aa4ab',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.416197',\n",
       "  'hid': 7,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a8d26acedf31aa4ab',\n",
       "  'dataset_id': 'bd7da0a40b8e2e82',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590758',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/006/SRR1658696/SRR1658696_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a58431f2c306da428',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a58431f2c306da428',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.512516',\n",
       "  'hid': 8,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a58431f2c306da428',\n",
       "  'dataset_id': '5d4cad9229129dd4',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590765',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/006/SRR1658696/SRR1658696_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33ae31293bf58ce91cc',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33ae31293bf58ce91cc',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.606758',\n",
       "  'hid': 9,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33ae31293bf58ce91cc',\n",
       "  'dataset_id': '77eb2251a7d90224',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590776',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/007/SRR1658697/SRR1658697_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aab9c831be03c165c',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aab9c831be03c165c',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.696337',\n",
       "  'hid': 10,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aab9c831be03c165c',\n",
       "  'dataset_id': 'f96d327d01b0f68e',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590789',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/007/SRR1658697/SRR1658697_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33acd8a00bea84dbd59',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33acd8a00bea84dbd59',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:08.803288',\n",
       "  'hid': 11,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33acd8a00bea84dbd59',\n",
       "  'dataset_id': '2fa78b90369b5a3e',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590796',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/008/SRR1658698/SRR1658698_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aba9287dcd29a8c2d',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aba9287dcd29a8c2d',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:09.060383',\n",
       "  'hid': 12,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aba9287dcd29a8c2d',\n",
       "  'dataset_id': '8073bb68c1c09740',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590820',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/008/SRR1658698/SRR1658698_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a7ed37826de74df7b',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a7ed37826de74df7b',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:09.191472',\n",
       "  'hid': 13,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a7ed37826de74df7b',\n",
       "  'dataset_id': '7b1a2245fe22442d',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590830',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/009/SRR1658699/SRR1658699_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a3d1e2c861bdf5363',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a3d1e2c861bdf5363',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:09.311644',\n",
       "  'hid': 14,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a3d1e2c861bdf5363',\n",
       "  'dataset_id': '94159eebc22d4ab7',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590837',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/009/SRR1658699/SRR1658699_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aa348cd617f7cbed5',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aa348cd617f7cbed5',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:09.414604',\n",
       "  'hid': 15,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aa348cd617f7cbed5',\n",
       "  'dataset_id': '00773230098acbdb',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590856',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/000/SRR1658700/SRR1658700_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aa5a32126c457ce07',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aa5a32126c457ce07',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:09.501503',\n",
       "  'hid': 16,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aa5a32126c457ce07',\n",
       "  'dataset_id': 'cec3206a0cc286a7',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590864',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/000/SRR1658700/SRR1658700_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33acd4fc96f6fd94039',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33acd4fc96f6fd94039',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:09.587143',\n",
       "  'hid': 17,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33acd4fc96f6fd94039',\n",
       "  'dataset_id': '470ef13a6a3077c0',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590871',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/001/SRR1658701/SRR1658701_1.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a9ea92eb443e40669',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a9ea92eb443e40669',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-05-21T09:04:09.667314',\n",
       "  'hid': 18,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a9ea92eb443e40669',\n",
       "  'dataset_id': '4b31f965850c0f50',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-05-22T12:17:55.590882',\n",
       "  'name': 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/001/SRR1658701/SRR1658701_2.fastq.gz',\n",
       "  'extension': 'fastqsanger.gz',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a5ca5c3f9bb24ae39',\n",
       "  'deleted': False,\n",
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       "  'update_time': '2019-06-19T15:37:03.396539',\n",
       "  'name': 'Bowtie2 on data 33: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a20907ae92514b8de',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a20907ae92514b8de',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:28.614967',\n",
       "  'hid': 85,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a20907ae92514b8de',\n",
       "  'dataset_id': '756487306c125ad9',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T08:45:58.924106',\n",
       "  'name': 'Bowtie2 on data 34: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a39dabdb46553718f',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a39dabdb46553718f',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:28.753516',\n",
       "  'hid': 86,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a39dabdb46553718f',\n",
       "  'dataset_id': '1befc1680d6cb67b',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:37:01.153720',\n",
       "  'name': 'Bowtie2 on data 34: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a5c31df81bace6205',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a5c31df81bace6205',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:28.800444',\n",
       "  'hid': 87,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a5c31df81bace6205',\n",
       "  'dataset_id': '5e40c4651b34e485',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T08:50:11.918759',\n",
       "  'name': 'Bowtie2 on data 35: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a90edc91b9a6c1997',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a90edc91b9a6c1997',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:28.952435',\n",
       "  'hid': 88,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a90edc91b9a6c1997',\n",
       "  'dataset_id': 'e948cab14c0356bc',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:36:59.199133',\n",
       "  'name': 'Bowtie2 on data 35: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a7882af64d8a02b90',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a7882af64d8a02b90',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:29.005490',\n",
       "  'hid': 89,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a7882af64d8a02b90',\n",
       "  'dataset_id': 'ececadca1b1c40d4',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T08:44:08.904200',\n",
       "  'name': 'Bowtie2 on data 36: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aa526056ff3efd569',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aa526056ff3efd569',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:29.226131',\n",
       "  'hid': 90,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aa526056ff3efd569',\n",
       "  'dataset_id': '674238b95c777777',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:36:57.853652',\n",
       "  'name': 'Bowtie2 on data 36: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a3f85963c9e23b11f',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a3f85963c9e23b11f',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:29.314596',\n",
       "  'hid': 91,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a3f85963c9e23b11f',\n",
       "  'dataset_id': 'f03becca8c966975',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T08:49:32.888736',\n",
       "  'name': 'Bowtie2 on data 37: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a314f6ac45796ecae',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a314f6ac45796ecae',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:29.469518',\n",
       "  'hid': 92,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a314f6ac45796ecae',\n",
       "  'dataset_id': '5357e41c60956fcb',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:36:55.948566',\n",
       "  'name': 'Bowtie2 on data 37: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33ae171f4fd59fbef7c',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33ae171f4fd59fbef7c',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:29.539909',\n",
       "  'hid': 93,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33ae171f4fd59fbef7c',\n",
       "  'dataset_id': 'f24d6b78c60a0dad',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T09:09:30.413555',\n",
       "  'name': 'Bowtie2 on data 38: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a20e040942d7d1031',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a20e040942d7d1031',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:29.776983',\n",
       "  'hid': 94,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a20e040942d7d1031',\n",
       "  'dataset_id': '26f9c4acdf994a87',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:36:53.673957',\n",
       "  'name': 'Bowtie2 on data 38: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a1c04808f1a037cb2',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a1c04808f1a037cb2',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:29.848164',\n",
       "  'hid': 95,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a1c04808f1a037cb2',\n",
       "  'dataset_id': '26baa750a266cbe5',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T09:03:17.295887',\n",
       "  'name': 'Bowtie2 on data 39: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a14bdf97bcb45ef79',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a14bdf97bcb45ef79',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:30.044093',\n",
       "  'hid': 96,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a14bdf97bcb45ef79',\n",
       "  'dataset_id': 'e8fe9f406c4db826',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:36:50.240398',\n",
       "  'name': 'Bowtie2 on data 39: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aba17c3b0593036e6',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aba17c3b0593036e6',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:30.116732',\n",
       "  'hid': 97,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aba17c3b0593036e6',\n",
       "  'dataset_id': '112d3b4d2fcedbf2',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T09:05:35.454603',\n",
       "  'name': 'Bowtie2 on data 40: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a76071109083daf2c',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a76071109083daf2c',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:30.325327',\n",
       "  'hid': 98,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a76071109083daf2c',\n",
       "  'dataset_id': 'd6806640a5198ac4',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:36:47.483917',\n",
       "  'name': 'Bowtie2 on data 40: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33aee2c93c30c8b8b15',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33aee2c93c30c8b8b15',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:30.382633',\n",
       "  'hid': 99,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33aee2c93c30c8b8b15',\n",
       "  'dataset_id': 'fe9e145978c192e5',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-18T09:12:48.737489',\n",
       "  'name': 'Bowtie2 on data 41: alignments',\n",
       "  'extension': 'bam',\n",
       "  'type_id': 'dataset-11ac94870d0bb33a632c2e7fffee70a4',\n",
       "  'deleted': False,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33a632c2e7fffee70a4',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:30.526223',\n",
       "  'hid': 100,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33a632c2e7fffee70a4',\n",
       "  'dataset_id': 'a84d2ead5113c2ca',\n",
       "  'type': 'file',\n",
       "  'purged': False},\n",
       " {'history_content_type': 'dataset',\n",
       "  'update_time': '2019-06-19T15:36:44.980334',\n",
       "  'name': 'Bowtie2 on data 41: mapping stats',\n",
       "  'extension': 'txt',\n",
       "  'type_id': 'dataset-11ac94870d0bb33af487d8a50cb8e30d',\n",
       "  'deleted': True,\n",
       "  'history_id': '629d1c15a670fb7c',\n",
       "  'tags': [],\n",
       "  'id': '11ac94870d0bb33af487d8a50cb8e30d',\n",
       "  'visible': True,\n",
       "  'state': 'ok',\n",
       "  'create_time': '2019-06-18T08:28:30.577203',\n",
       "  'hid': 101,\n",
       "  'url': '/api/histories/629d1c15a670fb7c/contents/11ac94870d0bb33af487d8a50cb8e30d',\n",
       "  'dataset_id': 'eff6fb5881b268df',\n",
       "  'type': 'file',\n",
       "  'purged': False}]"
      ]
     },
     "execution_count": 58,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "foo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'dataset'"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "foo[0]['history_content_type']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'history_content_type': 'dataset_collection', 'populated_state_message': None, 'name': '1kb matrices', 'populated': True, 'deleted': False, 'type': 'collection', 'history_id': '020f877513f2d0d1', 'tags': ['name:forward', 'name:reverse'], 'visible': True, 'job_source_id': '791bed8d7a1bddc8', 'job_source_type': 'ImplicitCollectionJobs', 'collection_type': 'list', 'url': '/api/histories/020f877513f2d0d1/contents/dataset_collections/fa8de3fed9a4f34b', 'model_class': 'HistoryDatasetCollectionAssociation', 'hid': 37548, 'element_count': 3883, 'id': 'fa8de3fed9a4f34b', 'populated_state': 'ok'}\n",
      "{'history_content_type': 'dataset_collection', 'populated_state_message': None, 'name': '10kb matrices', 'populated': True, 'deleted': False, 'type': 'collection', 'history_id': '020f877513f2d0d1', 'tags': ['name:forward', 'name:reverse'], 'visible': True, 'job_source_id': 'f561cb8e4ecc376a', 'job_source_type': 'ImplicitCollectionJobs', 'collection_type': 'list', 'url': '/api/histories/020f877513f2d0d1/contents/dataset_collections/97ad25f388508c0c', 'model_class': 'HistoryDatasetCollectionAssociation', 'hid': 37641, 'element_count': 3883, 'id': '97ad25f388508c0c', 'populated_state': 'ok'}\n"
     ]
    }
   ],
   "source": [
    "collections = []\n",
    "for i in foo:\n",
    "#     print(i)\n",
    "    if i['history_content_type'] == 'dataset_collection' and (i['name'] == '1kb matrices' or i['name'] == '10kb matrices'):\n",
    "        print(i)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "collection_10kb = gi.histories.show_dataset_collection('020f877513f2d0d1', '97ad25f388508c0c')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'11ac94870d0bb33a6c05d5b105c39374'"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "collection['elements'][0]['object']['id']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset_ids = []\n",
    "for dataset in collection['elements']:\n",
    "#     print(dataset)\n",
    "    dataset_ids.append(dataset['object']['id'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3883"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(dataset_ids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11ac94870d0bb33a6c05d5b105c39374\n",
      "11ac94870d0bb33a366dc87068e3534c\n",
      "11ac94870d0bb33a3b3ac7b4a6c7a7c3\n",
      "11ac94870d0bb33aaf5a2b5e97bb3b58\n",
      "11ac94870d0bb33aa295d9b26e4f0e81\n",
      "11ac94870d0bb33ae64f8f170566aff0\n",
      "11ac94870d0bb33a67d80c9c1ac7723d\n",
      "11ac94870d0bb33a6c04e00a58c88ba7\n",
      "11ac94870d0bb33a2091532a97caf12d\n",
      "11ac94870d0bb33a6499e01661bb50f9\n",
      "11ac94870d0bb33a8a5035843fb1215f\n",
      "11ac94870d0bb33a7dbaf50e835ef43a\n",
      "11ac94870d0bb33ad20c9bcfbd125dbe\n",
      "11ac94870d0bb33a9ebee204c419a830\n",
      "11ac94870d0bb33a5af9995e3af4bace\n",
      "11ac94870d0bb33a30fb575ade47b62b\n",
      "11ac94870d0bb33a937da6149e63449d\n",
      "11ac94870d0bb33a4c26c437d2a016d7\n",
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    {
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      "11ac94870d0bb33af60f29fd01362f2d\n",
      "11ac94870d0bb33aca5bbe025f1411c8\n",
      "11ac94870d0bb33aa850c6fc908788a5\n",
      "11ac94870d0bb33a02dd9f97ba58b96a\n",
      "11ac94870d0bb33a4ac4cf409b7ed7d9\n",
      "11ac94870d0bb33a99fe7f914c67cea4\n",
      "11ac94870d0bb33af1bf7b566e336040\n",
      "11ac94870d0bb33a9896bcdedab8b6d7\n",
      "11ac94870d0bb33ac6c1d6db722f00db\n",
      "11ac94870d0bb33a2e3f89db6b89e6a3\n",
      "11ac94870d0bb33aee2e45cf82eb6364\n",
      "11ac94870d0bb33a2ba5a532ef9aa07b\n",
      "11ac94870d0bb33ac61ebf1af3b4d175\n",
      "11ac94870d0bb33aa517398a33a44035\n",
      "11ac94870d0bb33aa5a1e5d5d0e35ceb\n",
      "11ac94870d0bb33a096874222a50a956\n",
      "11ac94870d0bb33aa3e283a79615fc13\n",
      "11ac94870d0bb33ad9312b9d3e7e55a9\n",
      "11ac94870d0bb33a6abdc2ad45013e0e\n",
      "11ac94870d0bb33ad8c58c2178e95de8\n"
     ]
    },
    {
     "ename": "DatasetStateException",
     "evalue": "Dataset state is not 'ok'. Dataset id: 11ac94870d0bb33ad8c58c2178e95de8, current state: error",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mDatasetStateException\u001b[0m                     Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-18-efc3eea52ccd>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mids\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdataset_ids\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mids\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m     \u001b[0mgi\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhistories\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdownload_dataset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'020f877513f2d0d1'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mids\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'/home/wolffj/sshfs/data/scHiC/10kb/'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/miniconda2/envs/schic/lib/python3.6/site-packages/bioblend/galaxy/histories/__init__.py\u001b[0m in \u001b[0;36mdownload_dataset\u001b[0;34m(self, history_id, dataset_id, file_path, use_default_filename)\u001b[0m\n\u001b[1;32m    427\u001b[0m         return self.gi.datasets.download_dataset(dataset_id,\n\u001b[1;32m    428\u001b[0m                                                  \u001b[0mfile_path\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mfile_local_path\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 429\u001b[0;31m                                                  use_default_filename=False)\n\u001b[0m\u001b[1;32m    430\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    431\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mdelete_history\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhistory_id\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpurge\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda2/envs/schic/lib/python3.6/site-packages/bioblend/galaxy/datasets/__init__.py\u001b[0m in \u001b[0;36mdownload_dataset\u001b[0;34m(self, dataset_id, file_path, use_default_filename, maxwait)\u001b[0m\n\u001b[1;32m     76\u001b[0m         \u001b[0mdataset\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_block_until_dataset_terminal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdataset_id\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmaxwait\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmaxwait\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     77\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mdataset\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'state'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'ok'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 78\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mDatasetStateException\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Dataset state is not 'ok'. Dataset id: %s, current state: %s\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mdataset_id\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdataset\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'state'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     79\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     80\u001b[0m         \u001b[0;31m# Galaxy release_13.01 and earlier does not have file_ext in the dataset\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mDatasetStateException\u001b[0m: Dataset state is not 'ok'. Dataset id: 11ac94870d0bb33ad8c58c2178e95de8, current state: error"
     ]
    }
   ],
   "source": [
    "for ids in dataset_ids:\n",
    "    print(ids)\n",
    "    gi.histories.download_dataset('020f877513f2d0d1', ids, '/home/wolffj/sshfs/data/scHiC/10kb/')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset_ids_10kb = []\n",
    "for dataset in collection_10kb['elements']:\n",
    "#     print(dataset)\n",
    "    dataset_ids_10kb.append(dataset['object']['id'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for ids in dataset_ids_10kb:\n",
    "#     print(ids)\n",
    "    gi.histories.download_dataset('020f877513f2d0d1', ids, '/home/wolffj/sshfs/data/scHiC/10kb_real/')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "id_history = '020f877513f2d0d1'\n",
    "# id_history = 'd5924a222c7a29de'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset_ids = gi.histories.show_history(id_history)['state_ids']['ok']\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7766"
      ]
     },
     "execution_count": 79,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(dataset_ids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['a963d38d5f3b4c95',\n",
       " 'ffe34bd0cff4601a',\n",
       " '446db129d08241c1',\n",
       " '0c895ae11adb0bec',\n",
       " '60b68a6afc5cc23b',\n",
       " 'c8d968db79649995',\n",
       " '689a2102215d30b9',\n",
       " '33d0743dda54decf']"
      ]
     },
     "execution_count": 70,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset_ids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "collection_description = {'collection_type': 'list',\n",
    " 'element_identifiers': [gi.histories.show_dataset(id_history, 'ffe34bd0cff4601a'),\n",
    "                         gi.histories.show_dataset(id_history, '0c895ae11adb0bec')],\n",
    " 'name': 'My collection list'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [],
   "source": [
    "element_identifiers_r1 = []\n",
    "element_identifiers_r2 = []\n",
    "for dataset_id in dataset_ids:\n",
    "    dataset_dict = gi.histories.show_dataset(id_history, dataset_id)\n",
    "    if '_R1.' in dataset_dict['name']:\n",
    "        element_identifiers_r1.append(dataset_dict)\n",
    "    elif '_R2.' in dataset_dict['name']:\n",
    "        element_identifiers_r2.append(dataset_dict)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3883"
      ]
     },
     "execution_count": 82,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(element_identifiers_r1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [],
   "source": [
    "collection_description_r1 = {'collection_type': 'list',\n",
    " 'element_identifiers': element_identifiers_r1,\n",
    " 'name': 'Forward reads'}\n",
    "collection_description_r2 = {'collection_type': 'list',\n",
    " 'element_identifiers': element_identifiers_r2,\n",
    " 'name': 'Reverse reads'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [],
   "source": [
    "bla = gi.histories.create_dataset_collection(id_history, collection_description_r1)\n",
    "bla2 = gi.histories.create_dataset_collection(id_history, collection_description_r2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(dataset_ids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['ffe34bd0cff4601a',\n",
       " '446db129d08241c1',\n",
       " '0c895ae11adb0bec',\n",
       " '60b68a6afc5cc23b']"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset_ids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [],
   "source": [
    "for dataset in dataset_ids:\n",
    "    name = gi.histories.show_dataset(id_history, dataset)['name']\n",
    "    gi.histories.update_dataset(id_history, dataset, tags=['name:'+name])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7766"
      ]
     },
     "execution_count": 59,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(names_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "names_list_ = names_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [],
   "source": [
    "names_list = names_list[:-1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "for dataset in dataset_ids[4792:]:\n",
    "    names_list.append(gi.histories.show_dataset(id_history, dataset)['name'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4792"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(names_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "for data_id, name in zip(dataset_ids[4792:], names_list[4792:]):\n",
    "    gi.histories.update_dataset(id_history, data_id, tags=['name:'+name])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'accessible': True,\n",
       " 'type_id': 'dataset-a16cfc87847903e0',\n",
       " 'file_name': '/data/dnb02/galaxy_db/files/009/207/dataset_9207095.dat',\n",
       " 'resubmitted': False,\n",
       " 'create_time': '2019-04-26T16:08:21.051777',\n",
       " 'creating_job': 'e655f8a8eda7d14d',\n",
       " 'dataset_id': '5167f28e365a349f',\n",
       " 'file_size': 184104998,\n",
       " 'file_ext': 'fastqsanger.gz',\n",
       " 'id': 'a16cfc87847903e0',\n",
       " 'misc_info': 'uploaded fastqsanger.gz file',\n",
       " 'hda_ldda': 'hda',\n",
       " 'download_url': '/api/histories/020f877513f2d0d1/contents/a16cfc87847903e0/display',\n",
       " 'state': 'ok',\n",
       " 'display_types': [],\n",
       " 'display_apps': [],\n",
       " 'metadata_dbkey': '?',\n",
       " 'type': 'file',\n",
       " 'misc_blurb': '175.6 MB',\n",
       " 'peek': '@HWI-D00436:144:HB8G5ADXX:1:1101:1860:2188/1\\n\\nAGATTGAAGGAATACAGTTGGCTGGGGTGACTAGATGTGTTGAAGATAGCTTTAACACGTAAGAATGAACCTGTCTCTTATACACATCTCCGAGCCCACGAGACACTCGCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAA\\n\\n+\\n\\nCCCFFDEFHHHHHJJJIHJJJJJJJJJHIHIJJIJJJFHIJIIJJJJJJJJJJIJJJJJGIJJJJJHHHHHFFFFFFEEEEDEEDDDDDDDDDDDDDDDDDBDDDDDDDDDDDA4>AB?BDDDDDBDDDDDDDDDDDDDDDDBD@######\\n\\n@HWI-D00436:144:HB8G5ADXX:1:1101:2724:2163/1\\n',\n",
       " 'update_time': '2019-04-29T15:36:56.014493',\n",
       " 'data_type': 'abc.FastqSangerGz',\n",
       " 'tags': ['name:Diploid_11_ACTCGCTA_AAGGCTAT_R1.fastq.gz'],\n",
       " 'deleted': False,\n",
       " 'history_id': '020f877513f2d0d1',\n",
       " 'meta_files': [],\n",
       " 'genome_build': '?',\n",
       " 'metadata_sequences': None,\n",
       " 'hid': 1,\n",
       " 'model_class': 'HistoryDatasetAssociation',\n",
       " 'metadata_data_lines': None,\n",
       " 'annotation': None,\n",
       " 'permissions': {'access': ['b9396694d489ce22'],\n",
       "  'manage': ['b9396694d489ce22']},\n",
       " 'history_content_type': 'dataset',\n",
       " 'name': 'Diploid_11_ACTCGCTA_AAGGCTAT_R1.fastq.gz',\n",
       " 'extension': 'fastqsanger.gz',\n",
       " 'visible': True,\n",
       " 'url': '/api/histories/020f877513f2d0d1/contents/a16cfc87847903e0',\n",
       " 'uuid': '8845fc6e-33d5-4014-bff5-5b702b27689a',\n",
       " 'visualizations': [{'description': None,\n",
       "   'embeddable': False,\n",
       "   'href': '/plugins/interactive_environments/jupyter/show',\n",
       "   'entry_point': {'type': 'mako', 'attr': {}, 'file': 'jupyter.mako'},\n",
       "   'groups': None,\n",
       "   'logo': None,\n",
       "   'specs': None,\n",
       "   'target': 'galaxy_main',\n",
       "   'name': 'jupyter',\n",
       "   'title': None,\n",
       "   'settings': None,\n",
       "   'html': 'Jupyter'}],\n",
       " 'rerunnable': False,\n",
       " 'purged': False,\n",
       " 'api_type': 'file'}"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gi.histories.update_dataset(id_history, dataset_ids[0], tags=['name:'+names_list[0] + ''])"
   ]
  }
 ],
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