upload.py

import biothings.hub.dataload.uploader
import os

import biothings
import config
import requests
biothings.config_for_app(config)

MAP_URL = "https://raw.githubusercontent.com/SuLab/outbreak.info-resources/master/outbreak_resources_es_mapping.json"
MAP_VARS = ["@type", "abstract", "alternateName", "armGroup", "author", "curatedBy", "date", "dateCreated", "dateModified", "datePublished", "description", "eligibilityCriteria", "hasResults", "healthCondition", "identifier", "identifierSource", "interventions", "interventionText", "isBasedOn", "keywords", "name", "outcome", "relatedTo", "funding", "studyDesign", "studyEvent", "studyLocation", "studyStatus", "url", "topicCategory"]

# when code is exported, import becomes relative
try:
    from covid_who_clinical_trials.parser import load_annotations as parser_func
except ImportError:
    from .parser import load_annotations as parser_func

logger = config.logger

class ClinicalTrialUploaderWHO(biothings.hub.dataload.uploader.BaseSourceUploader):
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        logger.warning("trial upload before crash")


    main_source = "covid_who_clinical_trials"
    name = "clinicaltrialswho"
    __metadata__ = {"src_meta": {
        "license_url": "https://www.who.int/about/who-we-are/publishing-policies/copyright",
        "url": "https://www.who.int/ictrp/en/"
    }}
    idconverter = None

    def load_data(self, data_folder):
        if data_folder:
            self.logger.info("Load data from directory: '%s'", data_folder)
        return parser_func()

    @classmethod
    def get_mapping(klass):
        r = requests.get(MAP_URL)
        if(r.status_code == 200):
            mapping = r.json()
            mapping_dict = { key: mapping[key] for key in MAP_VARS }
            return mapping_dict