FindDOIs.ipynb

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      "Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
      "Collecting python-docx\n",
      "  Downloading python-docx-0.8.11.tar.gz (5.6 MB)\n",
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      "\u001B[?25h  Preparing metadata (setup.py) ... \u001B[?25l\u001B[?25hdone\n",
      "Requirement already satisfied: lxml>=2.3.2 in /usr/local/lib/python3.8/dist-packages (from python-docx) (4.9.2)\n",
      "Building wheels for collected packages: python-docx\n",
      "  Building wheel for python-docx (setup.py) ... \u001B[?25l\u001B[?25hdone\n",
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      "Successfully built python-docx\n",
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  {
   "cell_type": "markdown",
   "source": "# Get DOIs from a list of citations",
   "metadata": {
    "id": "Rgi6eKLwNSsx"
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  {
   "cell_type": "markdown",
   "source": [
    "This takes a list of citations in a docx file and finds their DOIs using the CrossRef API. The first three cells import packages and define functions. Run them first; no output is expected."
   ],
   "metadata": {
    "id": "7HQq3RmiNysJ"
   }
  },
  {
   "cell_type": "code",
   "source": [
    "import requests\n",
    "from docx import Document\n",
    "from docx.shared import Pt\n",
    "from docx.enum.text import WD_COLOR_INDEX"
   ],
   "metadata": {
    "id": "eaFSxYp819zA",
    "executionInfo": {
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      "displayName": "Athitheya Gobinathan",
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   "execution_count": 2,
   "outputs": []
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  {
   "cell_type": "code",
   "source": [
    "def search(title, author, first_res=True):\n",
    "  title.replace(' ', '')\n",
    "  response = requests.get(f'https://api.crossref.org/works?query.title={title}&query.author={author}&select=DOI,author,title,volume,page')\n",
    "  first_res = None\n",
    "  for i in range(min(15, len(response.json()['message']['items']))):\n",
    "    article = response.json()['message']['items'][i]\n",
    "    if i == 0:\n",
    "      first_res = article\n",
    "    \n",
    "    if article['title'][0].lower() == title.lower():\n",
    "      return article\n",
    "    \n",
    "  if first_res:\n",
    "    return first_res\n",
    "  \n",
    "  return None"
   ],
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   "execution_count": 3,
   "outputs": []
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  {
   "cell_type": "code",
   "source": [
    "def get_dois(file, first_res):\n",
    "  articles = []\n",
    "  doc = Document(file)\n",
    "  for p in doc.paragraphs:\n",
    "    r = p.text\n",
    "    try:\n",
    "      author = r.split(',')[0]\n",
    "      title = r.split('). ')[1].split(\".\")[0]\n",
    "      article = search(title, author, first_res)\n",
    "      found_title =  article['title'][0]\n",
    "      found_first_author = article['author'][0]['family']\n",
    "      articles.append(\n",
    "          {\n",
    "              'orig_first_author': author,\n",
    "              'found_first_author': found_first_author,\n",
    "              'orig_title': title,\n",
    "              'found_title': found_title,\n",
    "              'doi': article['DOI']\n",
    "          }\n",
    "      )\n",
    "    except:\n",
    "      articles.append(\n",
    "          {\n",
    "              'orig_first_author': author,\n",
    "              'found_first_author': 'N/A',\n",
    "              'orig_title': title,\n",
    "              'found_title': 'N/A',\n",
    "              'doi': 'N/A'\n",
    "          }\n",
    "      )\n",
    "\n",
    "  return articles"
   ],
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   "execution_count": 4,
   "outputs": []
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   "cell_type": "markdown",
   "source": [
    "This is where the DOIs are retrieved.\n",
    "\n",
    "1. Drag your text file into the file directory (Click the file icon on the left sidebar, and then drag the file over the sidebar)\n",
    "\n",
    "2. Change the file name. You can either change your text file's name to 'ref_list.docx' or change the file name in the code snippet (line 2 of the code cell) below to your own file name\n",
    "\n",
    "3. Sometimes, the title in the citation and the title in the search result refer to the same article, but have slightly different formats or different first authors. If you want the formats to match exactly, you can set exact_match to 'True' (with an uppercase T) (line 3 of the code cell). I recommend keeping exact_match as 'False' (with an uppercase F) and looking through the CSV yourself to see if the DOI is correct for titles and authors that don't match. DOIs with mismatched authors/titles will also be highlighted in the new Word document.\n",
    "\n",
    "It's completely normal for the search to take a few minutes! You know it's done when there's a green checkmark next to the cell."
   ],
   "metadata": {
    "id": "-ZKRbA2iO3kX"
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  {
   "cell_type": "code",
   "source": [
    "import pandas as pd\n",
    "file = 'ref_list.docx'\n",
    "exact_match = False\n",
    "articles = get_dois(file, not exact_match)"
   ],
   "metadata": {
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   "execution_count": 5,
   "outputs": []
  },
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   "cell_type": "markdown",
   "source": [
    "View the output by running the cell below.\n",
    "\n",
    "The table has 5 columns. 'orig_first_author' and 'orig_title' refer to the author and title retrieved from the list of citations you imported. 'found_first_author' and 'found_title' refer to the citation that was found in the crossref database. 'N/A' values mean the article was not found. If the DOI was found, it will be in the last column\n",
    "\n",
    "It's important that you check original authors/titles and the found ones match! A mismatch does not always mean the wrong article was found (could be an error in the database)."
   ],
   "metadata": {
    "id": "Hceu7CwWQ95H"
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  {
   "cell_type": "code",
   "source": [
    "df = pd.DataFrame(articles)\n",
    "df"
   ],
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    "id": "EY95Bgy-R9lH",
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       "    orig_first_author found_first_author  \\\n",
       "0             Alberts              Hecht   \n",
       "1            Anderson                N/A   \n",
       "2              Ansell             Ansell   \n",
       "3              Arnett             Arnett   \n",
       "4             Bandura              Locke   \n",
       "..                ...                ...   \n",
       "122              Wong               Wong   \n",
       "123             Young              Young   \n",
       "124              Yuen               Yuen   \n",
       "125             Zador              Zador   \n",
       "126                                  N/A   \n",
       "\n",
       "                                            orig_title  \\\n",
       "0    The communicative process of drug resistance a...   \n",
       "1                Teens, Social Media & Technology 2018   \n",
       "2    Effects of marijuana use on impulsivity and ho...   \n",
       "3    Reckless driving in adolescence: ‘State’ and ‘...   \n",
       "4    Social Foundations of Thought and Action: A so...   \n",
       "..                                                 ...   \n",
       "122  Digital health technology to enhance adolescen...   \n",
       "123  Alcohol-related sexual assault victimization a...   \n",
       "124  Adolescent alcohol use trajectories: risk fact...   \n",
       "125  Alcohol-related relative risk of driver fatali...   \n",
       "126  Alcohol-related relative risk of driver fatali...   \n",
       "\n",
       "                                           found_title  \\\n",
       "0     Resistance to Drug Offers among College Students   \n",
       "1                                                  N/A   \n",
       "2    Effects of marijuana use on impulsivity and ho...   \n",
       "3    Reckless driving in adolescence: ‘State’ and ‘...   \n",
       "4    Social Foundations of Thought and Action: A So...   \n",
       "..                                                 ...   \n",
       "122  Digital Health Technology to Enhance Adolescen...   \n",
       "123  Alcohol-Related Sexual Assault Victimization A...   \n",
       "124  Adolescent Alcohol Use Trajectories: Risk Fact...   \n",
       "125  Alcohol-related relative risk of driver fatali...   \n",
       "126                                                N/A   \n",
       "\n",
       "                                  doi  \n",
       "0           10.3109/10826089209065589  \n",
       "1                                 N/A  \n",
       "2    10.1016/j.drugalcdep.2014.12.029  \n",
       "3       10.1016/s0001-4575(97)87007-8  \n",
       "4                      10.2307/258004  \n",
       "..                                ...  \n",
       "122  10.1016/j.jadohealth.2019.10.018  \n",
       "123          10.15288/jsad.2008.69.39  \n",
       "124            10.1542/peds.2020-0440  \n",
       "125          10.15288/jsa.2000.61.387  \n",
       "126                               N/A  \n",
       "\n",
       "[127 rows x 5 columns]"
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       "      <td>Alberts</td>\n",
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       "      <td>The communicative process of drug resistance a...</td>\n",
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       "      <td>Reckless driving in adolescence: ‘State’ and ‘...</td>\n",
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       "      <td>...</td>\n",
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       "      <th>122</th>\n",
       "      <td>Wong</td>\n",
       "      <td>Wong</td>\n",
       "      <td>Digital health technology to enhance adolescen...</td>\n",
       "      <td>Digital Health Technology to Enhance Adolescen...</td>\n",
       "      <td>10.1016/j.jadohealth.2019.10.018</td>\n",
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       "      <td>Adolescent Alcohol Use Trajectories: Risk Fact...</td>\n",
       "      <td>10.1542/peds.2020-0440</td>\n",
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       "      <th>125</th>\n",
       "      <td>Zador</td>\n",
       "      <td>Zador</td>\n",
       "      <td>Alcohol-related relative risk of driver fatali...</td>\n",
       "      <td>Alcohol-related relative risk of driver fatali...</td>\n",
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       "      <td></td>\n",
       "      <td>N/A</td>\n",
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       "      <td>N/A</td>\n",
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     "metadata": {},
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  {
   "cell_type": "markdown",
   "source": [
    "Now we'll write the dois into the word document and save it as 'ref_updated.docx'. It will show up in the same place you dragged your text file into (sometimes it takes a little bit for the files to show up). Insert_space determines whether or not to insert a space between the DOI and the citation. If your output file has 2 spaces between the DOI and citation, set this to 'False' (with an uppercase F).\n",
    "\n",
    "**IMPORTANT**: The dois that are highlighted in yellow MUST be double checked. These citations returned a different first author/title when obtained from the CrossRef database and may be incorrect.\n",
    "\n",
    "**UPDATE**: Set insert_space (line 2 of code cell) to 'False' (with an uppercase F) and run cell again if there are two spaces between the inserted DOI and the citation in the new docx file."
   ],
   "metadata": {
    "id": "8GSu8oNTTPzO"
   }
  },
  {
   "cell_type": "code",
   "source": [
    "doc = Document('ref_list.docx')\n",
    "insert_space = True\n",
    "\n",
    "i = 0\n",
    "miss = 0\n",
    "for p in doc.paragraphs:\n",
    "  try:\n",
    "    if 'doi' not in p.text:\n",
    "      if df.loc[i, 'doi'] != 'N/A':\n",
    "        \n",
    "        p.style.font.name = 'Times New Roman'\n",
    "        p.style.font.size = Pt(12)\n",
    "        title = df.loc[i, 'orig_title'].lower() \n",
    "        if title[-1] == '.':\n",
    "          title = title[:-1]\n",
    "        found = df.loc[i, 'found_title'].lower()\n",
    "        if found[-1] == '.':\n",
    "          found = found[:-1]\n",
    "        if df.loc[i, 'orig_first_author'].lower() == df.loc[i, 'found_first_author'].lower() and title == found:\n",
    "          if insert_space:\n",
    "            p.add_run(f\" doi:{df.loc[i, 'doi']}\")\n",
    "          else:\n",
    "            p.add_run(f\"doi:{df.loc[i, 'doi']}\")\n",
    "        else:\n",
    "          miss += 1\n",
    "          if insert_space:\n",
    "            p.add_run(f\" doi:{df.loc[i, 'doi']}\").font.highlight_color = WD_COLOR_INDEX.YELLOW\n",
    "          else:\n",
    "            p.add_run(f\"doi:{df.loc[i, 'doi']}\").font.highlight_color = WD_COLOR_INDEX.YELLOW\n",
    "    i += 1\n",
    "  except:\n",
    "    break\n",
    "  \n",
    "print(f\"Unsure about the DOIs of {miss} out of {i-1} citations.\")\n",
    "print(\"Saving...\")\n",
    "doc.save('refs_updated.docx')\n",
    "print(\"Saved!\")"
   ],
   "metadata": {
    "id": "CrXt0jBu66wr",
    "executionInfo": {
     "status": "ok",
     "timestamp": 1676553594106,
     "user_tz": 300,
     "elapsed": 292,
     "user": {
      "displayName": "Athitheya Gobinathan",
      "userId": "15483106227842522718"
     }
    },
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "outputId": "4727e42e-2680-49fd-ab52-9d330661e199"
   },
   "execution_count": 14,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": [
      "Unsure about the DOIs of 23 out of 126 citations.\n",
      "Saving...\n",
      "Saved!\n"
     ]
    }
   ]
  },
  {
   "cell_type": "markdown",
   "source": [
    "You can also export the table of ctiations to a CSV and Excel file. They will show up in the file tab with the rest of the files."
   ],
   "metadata": {
    "id": "JtjsealPUS6o"
   }
  },
  {
   "cell_type": "code",
   "source": [
    "df.to_csv('dois.csv')\n",
    "df.to_excel('dois.xlsx')"
   ],
   "metadata": {
    "id": "sClV90RgJTzL"
   },
   "execution_count": null,
   "outputs": []
  }
 ],
 "metadata": {
  "colab": {
   "provenance": []
  },
  "kernelspec": {
   "display_name": "Python 3",
   "name": "python3"
  },
  "language_info": {
   "name": "python"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}