02_Storage.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# eLABJournal and jupyter : storage\n",
    "Access to your eLABJournal samples from jupyter"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use the elabjournal package, create an object to access the API."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Welcome Matthijs Brouwer\n",
      "Package 'elabjournal', version '0.0.15'\n",
      "Your active group is 'Testgroup' (6727)\n"
     ]
    }
   ],
   "source": [
    "from elabjournal import elabjournal\n",
    "eLAB = elabjournal.api()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "#always use a specific group for this example\n",
    "eLAB.set_group(1056)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note: the storage calls can return both storage units and equipment. You can differentiate between the two with the storage type's deviceType field which is either STORAGE or EQUIPMENT. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Storage types"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A storage types object can be created that describes all the storage types."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Storage Types (23x)\n",
       "|\n",
       "|  Available methods, use help() on this object for more detailed information:\n",
       "|\n",
       "|  all(fields, maximum)\n",
       "|    Return all items in a single DataFrame.\n",
       "|  fields()\n",
       "|    Get the available fields.\n",
       "|  first(single)\n",
       "|    Get the first item (if exists).\n",
       "|  get(*args)\n",
       "|    Get the item for the provided index entry.\n",
       "|  name()\n",
       "|    Get the name.\n",
       "|  number()\n",
       "|    Get the number of items.\n",
       "|  show(fields, size)\n",
       "|    Create a browseable representation of the items.\n",
       "|  title()\n",
       "|    Get the title.\n",
       "|  visualize()\n",
       "|    Show visualization."
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "storageTypes = eLAB.storage_types()\n",
    "storageTypes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<g id=\"clust1\" class=\"cluster\">\n",
       "<title>cluster_object</title>\n",
       "<g id=\"a_clust1\"><a xlink:title=\"StorageType\">\n",
       "<polygon fill=\"#067172\" stroke=\"#000000\" points=\"8,-8 8,-82 210,-82 210,-8 8,-8\"/>\n",
       "<text text-anchor=\"middle\" x=\"109\" y=\"-66.8\" font-family=\"Times,serif\" font-size=\"14.00\" fill=\"#ffffff\">storageTypeID 13</text>\n",
       "</a>\n",
       "</g>\n",
       "</g>\n",
       "<!-- class_name -->\n",
       "<g id=\"node1\" class=\"node\">\n",
       "<title>class_name</title>\n",
       "<g id=\"a_node1\"><a xlink:title=\"StorageType\">\n",
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       "<text text-anchor=\"middle\" x=\"158\" y=\"-29.8\" font-family=\"Times,serif\" font-size=\"14.00\" fill=\"#ffffff\">&#45;150 Freezer</text>\n",
       "</a>\n",
       "</g>\n",
       "</g>\n",
       "<!-- class_type -->\n",
       "<g id=\"node2\" class=\"node\">\n",
       "<title>class_type</title>\n",
       "<g id=\"a_node2\"><a xlink:title=\"type\">\n",
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       "<text text-anchor=\"middle\" x=\"56\" y=\"-29.8\" font-family=\"Times,serif\" font-size=\"14.00\" fill=\"#ffffff\">STORAGE</text>\n",
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       "StorageType '-150 Freezer' (13)\n",
       "|\n",
       "|  Available methods, use help() on this object for more detailed information:\n",
       "|\n",
       "|  data()\n",
       "|    Get data.\n",
       "|  id()\n",
       "|    Get id.\n",
       "|  name()\n",
       "|    Get the name.\n",
       "|  show(fields)\n",
       "|    Create representation.\n",
       "|  storages()\n",
       "|    Get storages for this storage type.\n",
       "|  title()\n",
       "|    Get the title.\n",
       "|  type()\n",
       "|    Get deviceType.\n",
       "|  visualize()\n",
       "|    Create visualization."
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "storageType = storageTypes.first()\n",
    "display(storageType.visualize())\n",
    "storageType"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Storages"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A storages object can be created that describes all the storages."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Storages (13x)\n",
       "|\n",
       "|  Available methods, use help() on this object for more detailed information:\n",
       "|\n",
       "|  all(fields, maximum)\n",
       "|    Return all items in a single DataFrame.\n",
       "|  fields()\n",
       "|    Get the available fields.\n",
       "|  first(single)\n",
       "|    Get the first item (if exists).\n",
       "|  get(*args)\n",
       "|    Get the item for the provided index entry.\n",
       "|  name()\n",
       "|    Get the name.\n",
       "|  number()\n",
       "|    Get the number of items.\n",
       "|  show(fields, size)\n",
       "|    Create a browseable representation of the items.\n",
       "|  title()\n",
       "|    Get the title.\n",
       "|  visualize()\n",
       "|    Show visualization."
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#eLAB.storages(storageType)\n",
    "storages = eLAB.storages()\n",
    "storages"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "See `help(eLAB.storages)` for more options."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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       "<g id=\"clust1\" class=\"cluster\">\n",
       "<title>cluster_object</title>\n",
       "<g id=\"a_clust1\"><a xlink:title=\"Storage\">\n",
       "<polygon fill=\"#067172\" stroke=\"#000000\" points=\"8,-8 8,-82 190,-82 190,-8 8,-8\"/>\n",
       "<text text-anchor=\"middle\" x=\"99\" y=\"-66.8\" font-family=\"Times,serif\" font-size=\"14.00\" fill=\"#ffffff\">storageID 2826</text>\n",
       "</a>\n",
       "</g>\n",
       "</g>\n",
       "<g id=\"clust2\" class=\"cluster\">\n",
       "<title>cluster_type</title>\n",
       "<g id=\"a_clust2\"><a xlink:title=\"type of storage\">\n",
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       "</g>\n",
       "<!-- class_name -->\n",
       "<g id=\"node1\" class=\"node\">\n",
       "<title>class_name</title>\n",
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       "<text text-anchor=\"middle\" x=\"99\" y=\"-29.8\" font-family=\"Times,serif\" font-size=\"14.00\" fill=\"#ffffff\">LN2 storage unit F&#45;E0.967</text>\n",
       "</a>\n",
       "</g>\n",
       "</g>\n",
       "<!-- storage_type_name -->\n",
       "<g id=\"node2\" class=\"node\">\n",
       "<title>storage_type_name</title>\n",
       "<g id=\"a_node2\"><a xlink:title=\"type of storage\">\n",
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       "</a>\n",
       "</g>\n",
       "</g>\n",
       "<!-- storage_type_type -->\n",
       "<g id=\"node3\" class=\"node\">\n",
       "<title>storage_type_type</title>\n",
       "<g id=\"a_node3\"><a xlink:title=\"type of storage\">\n",
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       "<text text-anchor=\"middle\" x=\"246\" y=\"-29.8\" font-family=\"Times,serif\" font-size=\"14.00\" fill=\"#000000\">STORAGE</text>\n",
       "</a>\n",
       "</g>\n",
       "</g>\n",
       "<!-- storage_type_type&#45;&gt;class_name -->\n",
       "<g id=\"edge1\" class=\"edge\">\n",
       "<title>storage_type_type&#45;&gt;class_name</title>\n",
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    {
     "data": {
      "text/plain": [
       "Storage 'LN2 storage unit F-E0.967' (2826)\n",
       "|\n",
       "|  Available methods, use help() on this object for more detailed information:\n",
       "|\n",
       "|  barcode()\n",
       "|    Get the barcode of the storage (layer).\n",
       "|  data()\n",
       "|    Get data.\n",
       "|  id()\n",
       "|    Get id.\n",
       "|  name()\n",
       "|    Get the name.\n",
       "|  samples(*args, **kwargs)\n",
       "|    Get object to access samples for storage.\n",
       "|  show(fields)\n",
       "|    Create representation.\n",
       "|  statistics()\n",
       "|    Get statistics for storage.\n",
       "|  storage_layer()\n",
       "|    Get the storage layer.\n",
       "|  storage_type()\n",
       "|    Get the storage type.\n",
       "|  title()\n",
       "|    Get the title.\n",
       "|  visualize()\n",
       "|    Create visualization."
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "storage = storages.first()\n",
    "display(storage.visualize())\n",
    "storage"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get statistics for storage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "#storage.statistics()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get samples for storage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "#storageSamples = storage.samples()\n",
    "#storageSamples.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "See `help(eLAB.storages)` and `help(elabjournal.storage)` for more options."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Storage layers"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A storage layers object can be created that describes all the storage layers."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Storage Layers (1645x)\n",
       "|\n",
       "|  Available methods, use help() on this object for more detailed information:\n",
       "|\n",
       "|  all(fields, maximum)\n",
       "|    Return all items in a single DataFrame.\n",
       "|  fields()\n",
       "|    Get the available fields.\n",
       "|  first(single)\n",
       "|    Get the first item (if exists).\n",
       "|  get(*args)\n",
       "|    Get the item for the provided index entry.\n",
       "|  name()\n",
       "|    Get the name.\n",
       "|  number()\n",
       "|    Get the number of items.\n",
       "|  show(fields, size)\n",
       "|    Create a browseable representation of the items.\n",
       "|  title()\n",
       "|    Get the title.\n",
       "|  visualize()\n",
       "|    Show visualization."
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#storageLayers = eLAB.storage_layers(storage)\n",
    "storageLayers = eLAB.storage_layers()\n",
    "storageLayers"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get single storage layer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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       "<g id=\"clust1\" class=\"cluster\">\n",
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       "</g>\n",
       "<!-- class_name -->\n",
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       "<!-- storage_name -->\n",
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       "<title>storage_type_name</title>\n",
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       "</a>\n",
       "</g>\n",
       "</g>\n",
       "<!-- storage_type_type -->\n",
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       "<title>storage_type_type</title>\n",
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       "</g>\n",
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       "StorageLayer 'LN2 storage unit F-E0.967' (121761)\n",
       "|\n",
       "|  Available methods, use help() on this object for more detailed information:\n",
       "|\n",
       "|  barcode()\n",
       "|    Get the barcode of the storage layer.\n",
       "|  data()\n",
       "|    Get data.\n",
       "|  id()\n",
       "|    Get id.\n",
       "|  name()\n",
       "|    Get the name.\n",
       "|  parent()\n",
       "|    Get the parent as an object.\n",
       "|  show(fields)\n",
       "|    Create representation.\n",
       "|  storage()\n",
       "|    Get the storage as an object.\n",
       "|  title()\n",
       "|    Get the title.\n",
       "|  visualize()\n",
       "|    Create visualization."
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "storageLayer = storageLayers.first()\n",
    "display(storageLayer.visualize())\n",
    "storageLayer"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get storage layers with a specific storage layer as parent."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Storage Layers (22x)'"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "storageLayerChildren = eLAB.storage_layers(storageLayer)\n",
    "storageLayerChildren.title()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get parent storage layer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'LN2 storage unit F-E0.967'"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "storageLayerChildren.first().parent().name()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "#storageLayerExpanded = eLAB.storage_layer(storageLayer.id(), expand=\"statistics\")\n",
    "#storageLayerExpanded.data()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "See `help(eLAB.storage_layers)` and `help(elabjournal.storage_layer)` for more options."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Barcode\n",
    "For each **storage object**, the barcode method can be used to get the **storage layer** identifying barcode in an integer/string representation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LN2 storage unit F-E0.967\n",
      "008000000121761\n",
      "LN2 storage unit F-E0.967\n",
      "008000000121761\n"
     ]
    }
   ],
   "source": [
    "barcodeStorage = storage.barcode()\n",
    "print(storage.name())\n",
    "print(barcodeStorage)\n",
    "print(storage.storage_layer().name())\n",
    "print(storage.storage_layer().barcode())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'LN2 storage unit F-E0.967'"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "eLAB.barcode(barcodeStorage).name()"
   ]
  }
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