citation-generator/main.py at master · ying-li-python/citation-generator · GitHub

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"""
Writing citations for research papers is time-consuming! Luckily, Python can
access NCBI's database when we want to retrieve article information and help
create a citation in MLA format for the first five articles found.

Run the script in terminal:
$ python main.py

And then enter search terms to find the article you are looking for.
Enjoy!

"""


def pubmed_search(s):

    # import dependencies
    import requests

    # this is the base url of NCBI's Entrez API
    base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"

    # accessing NCBI database
    database = "pubmed"

    # build query url that is used to retrieve search results
    query_url = (
            base_url + "esearch.fcgi?db=" + database + "&term=" + s + "&retmode=json"
    )

    # request in response for the search information in JSON format
    response = requests.get(query_url).json()

    # idList itself is a list, create a string with the same name
    idList = response["esearchresult"]["idlist"]

    # set condition if no articles are found
    if len(idList) == 0:
        print("No articles found! Please try another search term.")

    # condition when article(s) are found
    else:
        # for loop to iterate the first five articles in idList
        for article in idList[0:5]:

            # count articles
            total = len(idList[0:5])

            # find the index of each article
            i = idList.index(article)

            # message to show the article search
            if i == 0:
                print("------------------------")
                print("Beginning article search")
                print("------------------------")

            # create article count. python index starts at 0 so we need to add 1
            article_count = int(i) + 1

            # count number of each article
            print(f"Retrieving articles {article_count} of {total}")

            # base url to retrieve article summary
            url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?"

            # generate endpoint url from our search to retrieve information for each article
            search_url = url + "db=" + database + "&id=" + article + "&retmode=json"

            # request article information, formatted as json
            search_response = requests.get(search_url).json()

            # create empty list for storing multiple authors per article
            author_list = []

            # try and except loop to keep the loop running
            try:

                # data parsing from our search response
                pubmed_id = search_response["result"][article]["uid"]
                title = search_response["result"][article]["title"]
                authors = search_response["result"][article]["authors"]
                journal = search_response["result"][article]["source"]
                pub_date = search_response["result"][article]["pubdate"]
                volume = search_response["result"][article]["volume"]
                issue = search_response["result"][article]["issue"]
                pages = search_response["result"][article]["pages"]
                doi = search_response["result"][article]["elocationid"]

                # append values to list
                for i in authors:
                    all_authors = i["name"]
                    author_list.append(all_authors)

                # replace [,], and ' symbols from each element in author list
                names = (
                    str(author_list).replace("'", "").replace("[", "").replace("]", "")
                )

                # replace italization in title with <i></i>
                corrected_title = title.replace("&lt;i&gt;", "<i>").replace(
                    "&lt;/i&gt;", "</i>"
                )

                # show results
                print(f"PubMed ID: {pubmed_id}")
                print(
                    f"{names}. {corrected_title} {journal} {pub_date[0:4]};{volume}({issue}):{pages}. {doi}"
                )
                print("------------------------")

            # create exception
            except ValueError:
                print("No information found. Skipping..")


# asks user for search terms
term = input("Please enter a search for PubMed articles: ").replace(" ", "+")

pubmed_search(term)