PacBio Report Example

report-example.ipynb

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   "source": [
    "import os\n",
    "import logging\n",
    "import random\n",
    "\n",
    "from pbcommand.models.report import Report, Attribute, PlotGroup, Table, Column, Plot\n",
    "\n",
    "log = logging.getLogger(__name__)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Create a Report Attribute "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def example_attributes():\n",
    "    a = Attribute('alpha', 1234, name='Alpha')\n",
    "    b = Attribute('beta', \"b-value\", name=\"Beta Display Name\")\n",
    "    return [a, b]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Attribute id:alpha value:1234 name:Alpha >,\n",
       " <Attribute id:beta value:b-value name:Beta Display Name >]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "example_attributes()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example Report Table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def example_tables():\n",
    "    \"\"\"Return a table with 2 columns\"\"\"\n",
    "    columns = [Column( 'c1id', header='C1 header'),\n",
    "            Column('c2id', header='C2 header')]\n",
    "\n",
    "    t = Table('myid', title='My Table', columns=columns)\n",
    "\n",
    "    #Now append data to the columns\n",
    "    #Assume data is a list of tuples of len == 2\n",
    "    datum = [(c.id, random.random()) for c in columns]\n",
    "    for column_id, value in datum:\n",
    "        t.add_data_by_column_id(column_id, value)\n",
    "\n",
    "    # Alternatively\n",
    "    cx = Column(\"cx\", header=\"X\", values=[1,2,3,4])\n",
    "    cy = Column(\"cy\", header=\"Y\", values=[1,4,9,16])\n",
    "    t2 = Table(\"xy\", title=\"X vs Y\", columns=[cx, cy])\n",
    "    return [t, t2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Table myid title:My Table ncolumns:2 >, <Table xy title:X vs Y ncolumns:2 >]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "example_tables()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Plot Group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def example_plotgroup():\n",
    "    \"\"\"Return a PlotGroup with 1 plot\"\"\"\n",
    "    # Image paths must be relative to the dir where the final Report is written\n",
    "\n",
    "    plot = Plot('plot_id', image='image.png', caption='this is a plot a description')\n",
    "    p = PlotGroup('pg_id', title='some title', thumbnail='image_thumb.png', plots=[plot])\n",
    "\n",
    "    return p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<PlotGroup id:pg_id title:some title nplots:1 >"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "example_plotgroup()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example Report"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def example_report():\n",
    "\n",
    "    tables = example_tables()\n",
    "    attributes = example_attributes()\n",
    "    plotgroup = example_plotgroup()\n",
    "    plotgroups = [plotgroup]\n",
    "\n",
    "    # Id must match ^[a-z0-9_]+$\n",
    "    r = Report('loading', title=\"Loading Report\",\n",
    "            attributes=attributes,\n",
    "            plotgroups=plotgroups,\n",
    "            tables=tables)\n",
    "    return r"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "r = example_report()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Report id:loading title:Loading Report uuid:b1f7f60e-dbf4-43a8-b49e-d7c36582fa29 nattributes:2 nplot_groups:1 ntables:2 >"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "r"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Table id:myid\n",
      "--------------------------------\n",
      "C1 header       C2 header       \n",
      "--------------------------------\n",
      "0.258159525326   0.999834193855  \n",
      "\n",
      "Table id:xy\n",
      "-------\n",
      "X  Y   \n",
      "-------\n",
      "1   1   \n",
      "2   4   \n",
      "3   9   \n",
      "4   16  \n"
     ]
    }
   ],
   "source": [
    "for t in r.tables:\n",
    "    print t"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<Attribute id:alpha value:1234 name:Alpha >\n",
      "<Attribute id:beta value:b-value name:Beta Display Name >\n"
     ]
    }
   ],
   "source": [
    "for a in r.attributes:\n",
    "    print a"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'b1f7f60e-dbf4-43a8-b49e-d7c36582fa29'"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "r.uuid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
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   "outputs": [],
   "source": []
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