Feed Zonedo metadata fields from Web of Science (WOS)

wos_to_zonedo_format.py

from wos import WosClient
from wos.utils import query
from bs4 import BeautifulSoup
from slugify import slugify
from iso639 import to_iso639_2
from suds.client import Client
import json


WOS_API_USER=""
WOS_API_PASS=""

def generate_metadata(wos_ids):
    """ 
    Fetch article metadata from Web of Science (WOS) API,
    parse it and format to Zonedo accepted structure. 
    You can POST it directly while create deposit but
    you have to handle Zonedo API requests yourself.
    
    Example output: https://yapistir.io/x2BE/Raw/
    """
    with WosClient('', '') as client:
        for wos_id in wos_ids:
            data = {}
            data["metadata"] = {}
            result = query(client, "UT=%s" % wos_id, '', 1, 1, 1)
            result = BeautifulSoup(result, "lxml")

            summary = result.records.rec.static_data.summary
            full = result.records.rec.static_data.fullrecord_metadata

            data["metadata"]["upload_type"] = 'publication'
            data["metadata"]["publication_type"] = 'article'
            data["metadata"]["license"] = "cc-by-sa"

            lang = full.languages.find("language", {"type": "primary"}).text
            data["metadata"]["language"] = to_iso639_2(lang, type='B')
            data["metadata"]["title"] = summary.titles.find("title", {"type": "item"}).text
            abstract = [str(p) for p in full.abstract.abstract_text.find_all("p")]
            data["metadata"]["description"] = "".join(abstract)
            try:
                data["metadata"]["doi"] = result.records.rec.dynamic_data.find("identifier", {"type": "doi"})["value"]
            except TypeError:
                pass

            if full.keywords:
                keywords = [keyword.text for keyword in full.keywords.find_all("keyword")]
                data["metadata"]["keywords"] = keywords

            data["metadata"]["journal_title"] = summary.titles.find("title", {"type": "source"}).text

            try:
                data["metadata"]["journal_volume"] = summary.pub_info["vol"]
            except KeyError:
                pass

            try:
                data["metadata"]["journal_issue"] = summary.pub_info["issue"]
            except KeyError:
                pass

            data["metadata"]["publication_date"] = summary.pub_info["sortdate"]

            try:
                data["metadata"]["journal_pages"] = "%s - %s" % (summary.page["begin"], summary.page["end"])
            except KeyError :
                pass

            creators = []
            affs = {}

            for address_name in full.addresses.find_all("address_name"):
                aff = address_name.find("organization", {"pref": "Y"}).text
                addr_no = address_name.address_spec["addr_no"]
                affs.update({addr_no: aff})

            for address_name in full.addresses.find_all("address_name"):
                names = address_name.find_all("name")
                for name in names:
                    creator = {}
                    creator["name"] = name.display_name.text
                    addr_no = name["addr_no"]
                    creator["affiliation"] = affs[addr_no]

                    contributors = result.records.rec.static_data.contributors

                    if contributors:
                        for contributor in contributors.find_all("contributor"):
                            if slugify(contributor.display_name.text) == slugify(name.display_name.text):
                                try:
                                    creator["orcid"] = contributor.find("name")["orcid_id"]
                                except KeyError:
                                    pass

                    creators.append(creator)

            data["metadata"]["creators"] = creators

            refs = []
            ref_obj = Client.dict(client.citedReferences(wos_id))
            for ref in ref_obj["references"]:
                try:

                    _author = ref["citedAuthor"]
                    author_last = _author.split(",")[0]
                    author_last = "%s%s" % (author_last[0], author_last[1:].lower())
                    author_first = _author.split(",")[1][1]
                    year = ref["year"]
                    title = ref["citedTitle"]
                    work = ref["citedWork"]
                    volume = ref["volume"]

                    ref = "%s, %s., [et al.] (%s) %s. %s, %s" % (author_last, author_first, year,  title, work, volume)
                    #ref = ref.upper()
                    refs.append(ref)
                except:
                    pass

            data["metadata"]["references"] = refs
            yield json.dumps(data)