notebooks/run-gear.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Run BIDS App Template on a Flywheel Instance"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The cell below will get a Flywheel client if you are logged in to a Flywheel instance.  It prints out the URL of the instance so you know where you are logged in."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'https://ss.ce.flywheel.io:443/api'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from datetime import datetime\n",
    "import flywheel\n",
    "fw = flywheel.Client('')\n",
    "fw.get_config().site.api_url"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Edit these constants to fit your situation.  The ID for the subject can be copied from the URL of a subject when you select it using the Flywheel platform.  This example runs the gear on a subject (as opposed to a project or session).  The Freesurfer license in set in the project's \"FREESURFER_LICENSE\" Custom Information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "GEAR_NAME = \"bids-app-template\"\n",
    "SUBJECT = \"5dc091c269d4f3002d16f334\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    },
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'0.0.0_0.3.15'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gear = fw.lookup(f\"gears/{GEAR_NAME}\")\n",
    "gear.gear.version"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'sub-TOME3024'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "subject = fw.get_subject(SUBJECT)\n",
    "subject.label"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "inputs = {}\n",
    "\n",
    "config = {\n",
    "    \"bids_app_args\": \"\",\n",
    "    \"example-bool-param\": False,\n",
    "    \"example-empty-param\": \"\",\n",
    "    \"example-threshold\": 3.1415926,\n",
    "    \"gear-dry-run\": False,\n",
    "    \"gear-ignore-bids-errors\": False,\n",
    "    \"gear-intermediate-files\": \"\",\n",
    "    \"gear-intermediate-folders\": \"\",\n",
    "    \"gear-keep-output\": False,\n",
    "    \"gear-log-level\": \"INFO\",\n",
    "    \"gear-run-bids-validation\": True,\n",
    "    \"gear-save-intermediate-output\": False,\n",
    "    \"verbose\": \"v\",\n",
    "    \"write-graph\": False\n",
    "}\n",
    "\n",
    "now = datetime.now()\n",
    "analysis_label = f'{gear.gear.name} {now.strftime(\"%m-%d-%Y %H:%M:%S\")} SDK launched'\n",
    "\n",
    "analysis_id = gear.run(analysis_label=analysis_label, config=config, inputs=inputs, destination=subject)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "def show_job_info(analysis_id):\n",
    "    now = datetime.now()\n",
    "    print(f'{now.strftime(\"%m-%d-%Y %H:%M:%S\")}')\n",
    "    print(f'analysis_id = {analysis_id}')\n",
    "    analysis = fw.get_analysis(analysis_id)\n",
    "    print(f'analysis.label = {analysis.label}')\n",
    "    job_id = analysis.job.id\n",
    "    print(f'job_id = {job_id}')\n",
    "    job = fw.get_job(job_id)\n",
    "    print(f'job.gear_info = {job.gear_info}')\n",
    "    print(f'job.state = {job.state}')\n",
    "    print(f'job.transitions = {job.transitions}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11-19-2020 17:54:55\n",
      "analysis_id = 5fb6f7a8b116da9bc035f134\n",
      "analysis.label = bids-app-template 11-19-2020 17:54:32 SDK launched\n",
      "job_id = 5fb6f7a8b116da9bc035f135\n",
      "job.gear_info = {'category': 'analysis',\n",
      " 'id': None,\n",
      " 'name': 'bids-app-template',\n",
      " 'version': '0.0.0_0.3.15'}\n",
      "job.state = running\n",
      "job.transitions = {'cancelled': None,\n",
      " 'complete': None,\n",
      " 'failed': None,\n",
      " 'running': datetime.datetime(2020, 11, 19, 22, 54, 35, 321000, tzinfo=tzutc())}\n"
     ]
    }
   ],
   "source": [
    "show_job_info(analysis_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11-19-2020 17:56:35\n",
      "analysis_id = 5fb6f7a8b116da9bc035f134\n",
      "analysis.label = bids-app-template 11-19-2020 17:54:32 SDK launched\n",
      "job_id = 5fb6f7a8b116da9bc035f135\n",
      "job.gear_info = {'category': 'analysis',\n",
      " 'id': None,\n",
      " 'name': 'bids-app-template',\n",
      " 'version': '0.0.0_0.3.15'}\n",
      "job.state = complete\n",
      "job.transitions = {'cancelled': None,\n",
      " 'complete': datetime.datetime(2020, 11, 19, 22, 54, 57, 485000, tzinfo=tzutc()),\n",
      " 'failed': None,\n",
      " 'running': datetime.datetime(2020, 11, 19, 22, 54, 35, 321000, tzinfo=tzutc())}\n"
     ]
    }
   ],
   "source": [
    "show_job_info(analysis_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'attempt': 1,\n",
       " 'config': {'config': {'bids_app_args': '',\n",
       "                       'example-bool-param': False,\n",
       "                       'example-empty-param': '',\n",
       "                       'example-threshold': 3.1415926,\n",
       "                       'gear-dry-run': False,\n",
       "                       'gear-ignore-bids-errors': False,\n",
       "                       'gear-intermediate-files': '',\n",
       "                       'gear-intermediate-folders': '',\n",
       "                       'gear-keep-output': False,\n",
       "                       'gear-log-level': 'INFO',\n",
       "                       'gear-run-bids-validation': True,\n",
       "                       'gear-save-intermediate-output': False,\n",
       "                       'verbose': 'v',\n",
       "                       'write-graph': False},\n",
       "            'destination': {'id': '5fb6f7a8b116da9bc035f134',\n",
       "                            'type': 'analysis'},\n",
       "            'inputs': {}},\n",
       " 'created': datetime.datetime(2020, 11, 19, 22, 54, 32, 950000, tzinfo=tzutc()),\n",
       " 'destination': {'id': '5fb6f7a8b116da9bc035f134', 'type': 'analysis'},\n",
       " 'gear_id': '5fb5a2f270bdffa34535f17a',\n",
       " 'gear_info': {'category': 'analysis',\n",
       "               'id': None,\n",
       "               'name': 'bids-app-template',\n",
       "               'version': '0.0.0_0.3.15'},\n",
       " 'id': '5fb6f7a8b116da9bc035f135',\n",
       " 'inputs': {},\n",
       " 'modified': datetime.datetime(2020, 11, 19, 22, 54, 57, 485000, tzinfo=tzutc()),\n",
       " 'origin': {'id': 'andyworth@flywheel.io', 'type': 'user'},\n",
       " 'outputs': [{'object': {'classification': {},\n",
       "                         'created': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'hash': 'v0-sha384-3ae3a014fe59f623ca9f9581376128a9435c2cc82f4c91d944da3a3b4251f95d5f3765fd9cb27e56e4483ffe8a125a49',\n",
       "                         'id': '7e834159-eeda-4eb5-8d7d-973ddd369948',\n",
       "                         'info': None,\n",
       "                         'info_exists': None,\n",
       "                         'mimetype': 'application/zip',\n",
       "                         'modality': None,\n",
       "                         'modified': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'name': 'index_5fb6f7a8b116da9bc035f134.html.zip',\n",
       "                         'origin': {'id': '5fb6f7a8b116da9bc035f135',\n",
       "                                    'method': None,\n",
       "                                    'name': None,\n",
       "                                    'type': 'job',\n",
       "                                    'via': None},\n",
       "                         'replaced': None,\n",
       "                         'size': 727,\n",
       "                         'tags': [],\n",
       "                         'type': 'archive',\n",
       "                         'zip_member_count': None},\n",
       "              'ref': {'id': '5fb6f7a8b116da9bc035f134',\n",
       "                      'name': 'index_5fb6f7a8b116da9bc035f134.html.zip',\n",
       "                      'type': 'analysis'}},\n",
       "             {'object': {'classification': {},\n",
       "                         'created': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'hash': 'v0-sha384-8f7f70b80d14b1e99ef7fc6980758a0c3829b9ae920a289294922b3b0be34f984a6e11a82539c630a4f771893d69a2fd',\n",
       "                         'id': '489e3203-c304-482c-87ff-f1f964c038b4',\n",
       "                         'info': None,\n",
       "                         'info_exists': None,\n",
       "                         'mimetype': 'application/zip',\n",
       "                         'modality': None,\n",
       "                         'modified': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'name': 'bids-app-template_sub-TOME3024_5fb6f7a8b116da9bc035f134.zip',\n",
       "                         'origin': {'id': '5fb6f7a8b116da9bc035f135',\n",
       "                                    'method': None,\n",
       "                                    'name': None,\n",
       "                                    'type': 'job',\n",
       "                                    'via': None},\n",
       "                         'replaced': None,\n",
       "                         'size': 3354,\n",
       "                         'tags': [],\n",
       "                         'type': 'archive',\n",
       "                         'zip_member_count': None},\n",
       "              'ref': {'id': '5fb6f7a8b116da9bc035f134',\n",
       "                      'name': 'bids-app-template_sub-TOME3024_5fb6f7a8b116da9bc035f134.zip',\n",
       "                      'type': 'analysis'}},\n",
       "             {'object': {'classification': {},\n",
       "                         'created': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'hash': 'v0-sha384-6edbdd7fa3f0948d995ad4893f88f2d70c7e19d71bd579ac69b5432ca0f2fbf0f47690d64bfef7804ac9284fb60f003c',\n",
       "                         'id': '765a4a12-65f7-48ba-853c-1c69a9bc3251',\n",
       "                         'info': None,\n",
       "                         'info_exists': None,\n",
       "                         'mimetype': 'text/html',\n",
       "                         'modality': None,\n",
       "                         'modified': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'name': 'bids_tree.html',\n",
       "                         'origin': {'id': '5fb6f7a8b116da9bc035f135',\n",
       "                                    'method': None,\n",
       "                                    'name': None,\n",
       "                                    'type': 'job',\n",
       "                                    'via': None},\n",
       "                         'replaced': None,\n",
       "                         'size': 1527,\n",
       "                         'tags': [],\n",
       "                         'type': 'markup',\n",
       "                         'zip_member_count': None},\n",
       "              'ref': {'id': '5fb6f7a8b116da9bc035f134',\n",
       "                      'name': 'bids_tree.html',\n",
       "                      'type': 'analysis'}},\n",
       "             {'object': {'classification': {},\n",
       "                         'created': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'hash': 'v0-sha384-3ae3a014fe59f623ca9f9581376128a9435c2cc82f4c91d944da3a3b4251f95d5f3765fd9cb27e56e4483ffe8a125a49',\n",
       "                         'id': '6241b17c-c153-48bf-bd97-a44998946a42',\n",
       "                         'info': None,\n",
       "                         'info_exists': None,\n",
       "                         'mimetype': 'application/zip',\n",
       "                         'modality': None,\n",
       "                         'modified': datetime.datetime(2020, 11, 19, 22, 54, 55, 797000, tzinfo=tzutc()),\n",
       "                         'name': 'bids_tree_5fb6f7a8b116da9bc035f134.html.zip',\n",
       "                         'origin': {'id': '5fb6f7a8b116da9bc035f135',\n",
       "                                    'method': None,\n",
       "                                    'name': None,\n",
       "                                    'type': 'job',\n",
       "                                    'via': None},\n",
       "                         'replaced': None,\n",
       "                         'size': 727,\n",
       "                         'tags': [],\n",
       "                         'type': 'archive',\n",
       "                         'zip_member_count': None},\n",
       "              'ref': {'id': '5fb6f7a8b116da9bc035f134',\n",
       "                      'name': 'bids_tree_5fb6f7a8b116da9bc035f134.html.zip',\n",
       "                      'type': 'analysis'}}],\n",
       " 'parent_info': {'acquisition': None,\n",
       "                 'analysis': {'id': '5fb6f7a8b116da9bc035f134',\n",
       "                              'label': 'bids-app-template 11-19-2020 17:54:32 '\n",
       "                                       'SDK launched'},\n",
       "                 'group': {'id': 'scien', 'label': 'Scientific Solutions'},\n",
       "                 'project': {'id': '5dc091c169d4f3002d16f32f',\n",
       "                             'label': 'BIDS_multi_session'},\n",
       "                 'session': None,\n",
       "                 'subject': {'id': '5dc091c269d4f3002d16f334',\n",
       "                             'label': 'sub-TOME3024'}},\n",
       " 'previous_job_id': None,\n",
       " 'request': {'inputs': [{'location': '/',\n",
       "                         'type': 'docker',\n",
       "                         'uri': 'ss.ce.flywheel.io/bids-app-template@sha256:e9fba368072e98e74d21a57e3ce584766f3a220c5add0528ba3bc804312bf8ff',\n",
       "                         'vu': None},\n",
       "                        {'location': '/flywheel/v0',\n",
       "                         'type': 'scitran',\n",
       "                         'uri': '/jobs/5fb6f7a8b116da9bc035f135/config.json',\n",
       "                         'vu': None}],\n",
       "             'outputs': [{'location': '/flywheel/v0/output',\n",
       "                          'type': 'scitran',\n",
       "                          'uri': '/engine?level=analysis&id=5fb6f7a8b116da9bc035f134&job=5fb6f7a8b116da9bc035f135'}],\n",
       "             'target': {'command': ['bash',\n",
       "                                    '-c',\n",
       "                                    '/usr/local/miniconda/bin/python run.py'],\n",
       "                        'dir': '/flywheel/v0',\n",
       "                        'env': {'FW_CONFIG_BIDS_APP_ARGS': '',\n",
       "                                'FW_CONFIG_EXAMPLEBOOLPARAM': 'false',\n",
       "                                'FW_CONFIG_EXAMPLEEMPTYPARAM': '',\n",
       "                                'FW_CONFIG_EXAMPLETHRESHOLD': '3.1415926',\n",
       "                                'FW_CONFIG_GEARDRYRUN': 'false',\n",
       "                                'FW_CONFIG_GEARIGNOREBIDSERRORS': 'false',\n",
       "                                'FW_CONFIG_GEARINTERMEDIATEFILES': '',\n",
       "                                'FW_CONFIG_GEARINTERMEDIATEFOLDERS': '',\n",
       "                                'FW_CONFIG_GEARKEEPOUTPUT': 'false',\n",
       "                                'FW_CONFIG_GEARLOGLEVEL': 'INFO',\n",
       "                                'FW_CONFIG_GEARRUNBIDSVALIDATION': 'true',\n",
       "                                'FW_CONFIG_GEARSAVEINTERMEDIATEOUTPUT': 'false',\n",
       "                                'FW_CONFIG_VERBOSE': 'v',\n",
       "                                'FW_CONFIG_WRITEGRAPH': 'false',\n",
       "                                'PATH': '/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin',\n",
       "                                'PYTHONUNBUFFERED': '1'}}},\n",
       " 'retried': None,\n",
       " 'state': 'complete',\n",
       " 'tags': ['analysis', 'bids-app-template']}"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job_id = \"5fb6f7a8b116da9bc035f135\"\n",
    "detail = fw.get_job_detail(job_id)\n",
    "detail"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'id': None,\n",
       " 'logs': [{'fd': -1,\n",
       "           'msg': 'Gear Name: bids-app-template, Gear Version: 0.0.0_0.3.15\\n'},\n",
       "          {'fd': -1, 'msg': 'Gear starting...\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO flywheel_gear_toolkit.logging] '\n",
       "                  'Log level is INFO\\n'\n",
       "                  '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Destination is '\n",
       "                  'analysis=5fb6f7a8b116da9bc035f134\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"bids_app_args=\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"example-bool-param=False\"\\n'\n",
       "                  '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"example-empty-param=\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"example-threshold=3.1415926\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-dry-run=False\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-ignore-bids-errors=False\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-intermediate-files=\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-intermediate-folders=\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-keep-output=False\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-log-level=INFO\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-run-bids-validation=True\"\\n'\n",
       "                  '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"gear-save-intermediate-output=False\"\\n'\n",
       "                  '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"verbose=v\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:35     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Config '\n",
       "                  '\"write-graph=False\"\\n'},\n",
       "          {'fd': 2,\n",
       "           'msg': '/usr/local/miniconda/lib/python3.8/site-packages/flywheel/flywheel.py:6215: '\n",
       "                  'UserWarning: Client version 14.3.3 does not match server '\n",
       "                  'version 12.4.5. Please update your client version!\\n'\n",
       "                  \"  warnings.warn('Client version {} does not match server \"\n",
       "                  'version {}. Please update your client '\n",
       "                  \"version!'.format(SDK_VERSION, release_version))\\n\"},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36  WARNING Flywheel] Use \"pip install '\n",
       "                  'flywheel-sdk~=12.4.5\" to install a compatible version for '\n",
       "                  'this server\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO utils.bids.run_level] Gear run '\n",
       "                  \"level and hierarchy labels: {'run_level': 'subject', \"\n",
       "                  \"'run_label': 'sub-TOME3024', 'group': 'scien', \"\n",
       "                  \"'project_label': 'BIDS_multi_session', 'subject_label': \"\n",
       "                  \"'sub-TOME3024', 'session_label': None, 'acquisition_label': \"\n",
       "                  'None}\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO '\n",
       "                  'utils.fly.set_performance_config] os.cpu_count() = 4\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO '\n",
       "                  'utils.fly.set_performance_config] using n_cpus = 4 (maximum '\n",
       "                  'available)\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO '\n",
       "                  'utils.fly.set_performance_config] '\n",
       "                  'psutil.virtual_memory().available= 14.00 GiB\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO '\n",
       "                  'utils.fly.set_performance_config] using mem_gb = 14 '\n",
       "                  '(maximum available)\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO utils.freesurfer] Using '\n",
       "                  'FreeSurfer license in project info.\\n'},\n",
       "          {'fd': 1, 'msg': 'num_things = None\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36  WARNING '\n",
       "                  'flywheel_gear_toolkit.interfaces.command_line] Removing '\n",
       "                  'parameter with empty value for key \"example-bool-param\".\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36  WARNING '\n",
       "                  'flywheel_gear_toolkit.interfaces.command_line] Removing '\n",
       "                  'parameter with empty value for key '\n",
       "                  '\"example-empty-param\".\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36  WARNING '\n",
       "                  'flywheel_gear_toolkit.interfaces.command_line] Removing '\n",
       "                  'parameter with empty value for key \"write-graph\".\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO __main__] command is: '\n",
       "                  \"['./tests/test.sh', '/flywheel/v0/work/bids', \"\n",
       "                  \"'/flywheel/v0/output/5fb6f7a8b116da9bc035f134', \"\n",
       "                  \"'participant', '', '--example-threshold=3.1415926', '-v', \"\n",
       "                  \"'--n_cpus=4', '--mem_gb=14']\\n\"},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO utils.bids.download_run_level] '\n",
       "                  'Not downloading source data.\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO utils.bids.download_run_level] '\n",
       "                  'Dry run is NOT set.  Data WILL be downloaded.\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO utils.bids.download_run_level] '\n",
       "                  'Downloading BIDS data in all folders.\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO utils.bids.download_run_level] '\n",
       "                  'Downloading BIDS for subject \"sub-TOME3024\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:36     INFO '\n",
       "                  'flywheel_gear_toolkit.context.context] Using source '\n",
       "                  'container: project=5dc091c169d4f3002d16f32f\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Processing '\n",
       "                  'project files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Processing '\n",
       "                  'session files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Processing '\n",
       "                  'acquisition files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Processing '\n",
       "                  'acquisition files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Processing '\n",
       "                  'acquisition files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Downloading '\n",
       "                  'project files\\n'\n",
       "                  '[ 20201119 22:54:37     INFO bids-exporter] Downloading '\n",
       "                  'session files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Downloading '\n",
       "                  'acquisition files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Downloading '\n",
       "                  'acquisition file: '\n",
       "                  'sub-TOME3024_ses-Session1_dir-PA_epi.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:37     INFO bids-exporter] Downloading '\n",
       "                  'acquisition file: '\n",
       "                  'sub-TOME3024_ses-Session1_dir-AP_epi.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:38     INFO bids-exporter] Downloading '\n",
       "                  'acquisition file: '\n",
       "                  'sub-TOME3024_ses-Session1_task-REST_dir-AP_run-1_sbref.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:38     INFO bids-exporter] Downloading '\n",
       "                  'acquisition file: '\n",
       "                  'sub-TOME3024_ses-Session1_task-REST_dir-AP_run-2_bold.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO bids-exporter] Downloading '\n",
       "                  'acquisition file: '\n",
       "                  'sub-TOME3024_ses-Session2_acq-MPR_T1w.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO bids-exporter] Creating '\n",
       "                  'sidecar files\\n'\n",
       "                  '[ 20201119 22:54:52     INFO bids-exporter] Creating '\n",
       "                  'sidecar file: '\n",
       "                  '/flywheel/v0/work/bids/dataset_description.json\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO bids-exporter] Creating '\n",
       "                  'sidecar file: '\n",
       "                  '/flywheel/v0/work/bids/sub-TOME3024/ses-Session1/fmap/sub-TOME3024_ses-Session1_dir-PA_epi.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO bids-exporter] Creating '\n",
       "                  'sidecar file: '\n",
       "                  '/flywheel/v0/work/bids/sub-TOME3024/ses-Session1/fmap/sub-TOME3024_ses-Session1_dir-AP_epi.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO bids-exporter] Creating '\n",
       "                  'sidecar file: '\n",
       "                  '/flywheel/v0/work/bids/sub-TOME3024/ses-Session1/func/sub-TOME3024_ses-Session1_task-REST_dir-AP_run-1_sbref.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO bids-exporter] Creating '\n",
       "                  'sidecar file: '\n",
       "                  '/flywheel/v0/work/bids/sub-TOME3024/ses-Session1/func/sub-TOME3024_ses-Session1_task-REST_dir-AP_run-2_bold.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO bids-exporter] Creating '\n",
       "                  'sidecar file: '\n",
       "                  '/flywheel/v0/work/bids/sub-TOME3024/ses-Session2/anat/sub-TOME3024_ses-Session2_acq-MPRHA_T1w.nii.gz\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO utils.bids.download_run_level] '\n",
       "                  'Found BIDS path /flywheel/v0/work/bids\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO utils.bids.download_run_level] '\n",
       "                  \"type of Funding is: <class 'str'>\\n\"},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52  WARNING utils.bids.download_run_level] '\n",
       "                  'data[\"Funding\"] is not a list\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO utils.bids.download_run_level] '\n",
       "                  \"changed it to: <class 'list'>\\n\"},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:52     INFO utils.bids.validate] Command: '\n",
       "                  'bids-validator --verbose --json /flywheel/v0/work/bids\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.bids.validate] '\n",
       "                  'bids-validator return code: 0\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.bids.validate] '\n",
       "                  'bids-validator results:\\n'\n",
       "                  '\\n'\n",
       "                  'Valid BIDS files summary:\\n'\n",
       "                  \"{       'dataProcessed': False,\\n\"\n",
       "                  \"        'modalities': ['sbref', 'bold', 'T1w', \"\n",
       "                  \"'fieldmap'],\\n\"\n",
       "                  \"        'sessions': ['Session1', 'Session2'],\\n\"\n",
       "                  \"        'size': 560115759,\\n\"\n",
       "                  \"        'subjects': ['TOME3024'],\\n\"\n",
       "                  \"        'tasks': ['REST'],\\n\"\n",
       "                  \"        'totalFiles': 11}\\n\"\n",
       "                  '\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55  WARNING utils.bids.validate] Task '\n",
       "                  'scans should have a corresponding events.tsv file. If this '\n",
       "                  'is a resting state scan you can ignore this warning or '\n",
       "                  'rename the task to include the word \"rest\".\\n'\n",
       "                  '      '\n",
       "                  '/sub-TOME3024/ses-Session1/func/sub-TOME3024_ses-Session1_task-REST_dir-AP_run-2_bold.nii.gz\\n'\n",
       "                  '\\n'\n",
       "                  '[ 20201119 22:54:55  WARNING utils.bids.validate] The '\n",
       "                  'recommended file /README is missing. See Section 03 '\n",
       "                  '(Modality agnostic files) of the BIDS specification.\\n'\n",
       "                  '\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55  WARNING utils.bids.validate] The '\n",
       "                  'Authors field of dataset_description.json should contain an '\n",
       "                  'array of fields - with one author per field. This was '\n",
       "                  'triggered because there are no authors, which will make DOI '\n",
       "                  'registration from dataset metadata impossible.\\n'\n",
       "                  '\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.bids.download_run_level] '\n",
       "                  'Downloading BIDS data was successful!\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.bids.tree] Getting '\n",
       "                  '\"tree\" listing of /flywheel/v0/work/bids/\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.bids.tree] Wrote '\n",
       "                  '\"/flywheel/v0/output/bids_tree.html\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO __main__] Creating output '\n",
       "                  'directory /flywheel/v0/output/5fb6f7a8b116da9bc035f134\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO '\n",
       "                  'flywheel_gear_toolkit.interfaces.command_line] Executing '\n",
       "                  'command: \\n'\n",
       "                  ' ./tests/test.sh /flywheel/v0/work/bids '\n",
       "                  '/flywheel/v0/output/5fb6f7a8b116da9bc035f134 participant  '\n",
       "                  '--example-threshold=3.1415926 -v --n_cpus=4 --mem_gb=14 \\n'\n",
       "                  '\\n'\n",
       "                  '\\n'},\n",
       "          {'fd': 1, 'msg': 'Python 3.9.0\\n\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': 'add html files to find in '\n",
       "                  '/flywheel/v0/output/5fb6f7a8b116da9bc035f134\\n'\n",
       "                  '\\n'},\n",
       "          {'fd': 1, 'msg': 'ls \\n\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': 'Dockerfile\\n'\n",
       "                  '\\n'\n",
       "                  'LICENSE\\n'\n",
       "                  '\\n'\n",
       "                  'README.md\\n'\n",
       "                  '\\n'\n",
       "                  'config.json\\n'\n",
       "                  '\\n'\n",
       "                  'manifest.json\\n'\n",
       "                  '\\n'\n",
       "                  'output\\n'\n",
       "                  '\\n'\n",
       "                  'requirements.txt\\n'\n",
       "                  '\\n'\n",
       "                  'run.py\\n'\n",
       "                  '\\n'\n",
       "                  'setup.cfg\\n'\n",
       "                  '\\n'\n",
       "                  'tests\\n'\n",
       "                  '\\n'\n",
       "                  'utils\\n'\n",
       "                  '\\n'\n",
       "                  'work\\n'\n",
       "                  '\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': 'arguments: /flywheel/v0/work/bids '\n",
       "                  '/flywheel/v0/output/5fb6f7a8b116da9bc035f134 participant '\n",
       "                  '--example-threshold=3.1415926 -v --n_cpus=4 --mem_gb=14\\n'\n",
       "                  '\\n'\n",
       "                  '--example-threshold=3.1415926 -v --n_cpus=4\\n'\n",
       "                  '\\n'},\n",
       "          {'fd': 1, 'msg': 'I will not generate an error\\n\\n'},\n",
       "          {'fd': 1, 'msg': 'test.sh is done\\n'},\n",
       "          {'fd': 1, 'msg': '\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO '\n",
       "                  'flywheel_gear_toolkit.interfaces.command_line] Command '\n",
       "                  'return code: 0\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO '\n",
       "                  'flywheel_gear_toolkit.utils.zip_tools] Zipping output file '\n",
       "                  'bids-app-template_sub-TOME3024_5fb6f7a8b116da9bc035f134.zip\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.results.zip_htmls] '\n",
       "                  'Creating viewable archives for all html files\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.results.zip_htmls] Found '\n",
       "                  'path: /flywheel/v0/output/5fb6f7a8b116da9bc035f134\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.results.zip_htmls] Found '\n",
       "                  'index.html\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.results.zip_htmls] '\n",
       "                  'Creating viewable archive '\n",
       "                  '\"/flywheel/v0/output/index_5fb6f7a8b116da9bc035f134.html.zip\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO utils.results.zip_htmls] '\n",
       "                  'Creating viewable archive '\n",
       "                  '\"/flywheel/v0/output/bids_tree_5fb6f7a8b116da9bc035f134.html.zip\"\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO __main__] Wrote '\n",
       "                  '/flywheel/v0/output/.metadata.json\\n'},\n",
       "          {'fd': 1,\n",
       "           'msg': '[ 20201119 22:54:55     INFO __main__] '\n",
       "                  'flywheel-apps/bids-app-template] Gear is done.  Returning '\n",
       "                  '0\\n'},\n",
       "          {'fd': -1,\n",
       "           'msg': 'Gear completed successfully after running for 20.352s.\\n'},\n",
       "          {'fd': -1, 'msg': 'Uploading results...\\n'},\n",
       "          {'fd': -1, 'msg': 'Job complete.\\n'},\n",
       "          {'fd': -1, 'msg': 'The following outputs have been saved:\\n'},\n",
       "          {'fd': -1, 'msg': '  - index_5fb6f7a8b116da9bc035f134.html.zip\\n'},\n",
       "          {'fd': -1,\n",
       "           'msg': '  - '\n",
       "                  'bids-app-template_sub-TOME3024_5fb6f7a8b116da9bc035f134.zip\\n'},\n",
       "          {'fd': -1, 'msg': '  - bids_tree.html\\n'},\n",
       "          {'fd': -1,\n",
       "           'msg': '  - bids_tree_5fb6f7a8b116da9bc035f134.html.zip\\n'}]}"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job_logs = fw.get_job_logs(job_id)\n",
    "job_logs"
   ]
  }
 ],
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