How to use the biothings.hub.dataload.uploader.DummySourceUploader function in biothings

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github biothings / mygene.info / src / hub / dataload / sources / wikipedia / upload.py View on Github external
import biothings.hub.dataload.uploader as uploader

class WikipediaUploader(uploader.DummySourceUploader):

    name = "wikipedia"

    @classmethod
    def get_mapping(klass):
        mapping = {
                "wikipedia": {
                    "dynamic": False,
                    "properties": {
                        "url_stub": {
                            "type": "text",
                            'copy_to': ['all'],
                            }
                        }
                    }
                }
github biothings / mygene.info / src / hub / dataload / sources / uniprot / ipi_upload.py View on Github external
import biothings.hub.dataload.uploader as uploader

class UniprotIPIUploader(uploader.DummySourceUploader):
    """
    Discontinued, last release was: 20140611
    """

    name = "uniprot_ipi"


    @classmethod
    def get_mapping(klass):
        mapping = {
                "ipi" : {
                    "type" : "keyword",
                    "normalizer" : "keyword_lowercase_normalizer",
                    'copy_to': ['all'],
                    }
                }
github biothings / myvariant.info / src / hub / dataload / sources / cadd / cadd_upload.py View on Github external
from .cadd_parser import load_data
import biothings.hub.dataload.uploader as uploader
from hub.dataload.uploader import SnpeffPostUpdateUploader

class CADDUploader(uploader.DummySourceUploader, SnpeffPostUpdateUploader):

    keep_archive = 1

    name = "cadd"
    __metadata__ = {
        "assembly" : "hg19",
        "src_meta" : {
            "url" : "http://cadd.gs.washington.edu/home",
            "license_url" : "http://cadd.gs.washington.edu/contact",
            "license_url_short": "http://bit.ly/2TIuab9"
        }
    }

    def load_data(self,data_folder):
        self.logger.info("Load data from folder '%s'" % data_folder)
        return load_data(data_folder)
github biothings / myvariant.info / src / hub / dataload / sources / mutdb / mutdb_upload.py View on Github external
import biothings.hub.dataload.uploader as uploader
from hub.dataload.uploader import SnpeffPostUpdateUploader

class MutDBUploader(uploader.DummySourceUploader,SnpeffPostUpdateUploader):
    """Originally downloaded from: http://www.mutdb.org/"""

    name = "mutdb"
    __metadata__ = {
        "mapper" : 'observed',
        "assembly" : "hg19",
        "src_meta" : {
            "url" : "http://www.mutdb.org/",
            "license_url" : "http://www.mutdb.org/",
            "license_url_short": "http://bit.ly/2SQ6fXA"
        }
    }

    @classmethod
    def get_mapping(klass):
        mapping = {
github biothings / myvariant.info / src / hub / dataload / sources / cosmic / cosmic_upload.py View on Github external
import biothings.hub.dataload.uploader as uploader
from hub.dataload.uploader import SnpeffPostUpdateUploader

class CosmicUploader(uploader.DummySourceUploader,SnpeffPostUpdateUploader):

    name = "cosmic"
    __metadata__ = {
        "mapper" : 'observed',
        "assembly" : "hg19",
        "src_meta" : {
            "url" : "http://cancer.sanger.ac.uk/cosmic",
            "license_url" : "http://cancer.sanger.ac.uk/cosmic/license",
            "license_url_short": "http://bit.ly/2VMkY7R",
            "note": "COSMIC v68 was imported from UCSC database dump. This is the last freely available somatic variants from COSMIC before their licence change."
        }
    }

    @classmethod
    def get_mapping(klass):
        mapping = {
github biothings / mygene.info / src / hub / dataload / sources / ensembl / genomic_pos_hg19_upload.py View on Github external
import biothings.hub.dataload.uploader as uploader

class EnsemblGenomicPosHg19Uploader(uploader.DummySourceUploader):

    name = "ensembl_genomic_pos_hg19"

    @classmethod
    def get_mapping(klass):
        mapping = {
                "genomic_pos_hg19" : {
                    "dynamic" : False,
                    "type" : "nested",
                    "properties" : {
                        "start" : {
                            "type" : "long"
                            },
                        "chr" : {
                            "normalizer" : "keyword_lowercase_normalizer",
                            "type": "keyword"
github biothings / mygene.info / src / hub / dataload / sources / unigene / unigene_upload.py View on Github external
import biothings.hub.dataload.uploader as uploader


class EntrezUnigeneUploader(uploader.DummySourceUploader):

    name = "entrez_unigene"

    @classmethod
    def get_mapping(klass):
        mapping = {
            "unigene":  {
                "type": "keyword",
                "normalizer" : "keyword_lowercase_normalizer",
                'copy_to': ['all']
            }
        }
        return mapping
github biothings / myvariant.info / src / hub / dataload / sources / snpedia / snpedia_upload.py View on Github external
import biothings.hub.dataload.uploader as uploader
from hub.dataload.uploader import SnpeffPostUpdateUploader

class SnpediaUploader(uploader.DummySourceUploader,SnpeffPostUpdateUploader):
    """Originally downloaded from: http://www.snpedia.org/"""

    name = "snpedia"
    __metadata__ = {
        "mapper" : 'observed',
        "assembly" : "hg19",
        "src_meta" : {
            "url" : "https://www.snpedia.com/",
            "license" : "CC BY-NC-SA",
            "license_url" : "https://www.snpedia.com/index.php/SNPedia:General_disclaimer",
            "license_url_short": "http://bit.ly/2VJ3TeR"
        }
    }

    @classmethod
    def get_mapping(klass):
github biothings / mygene.info / src / hub / dataload / sources / pharos / upload.py View on Github external
import biothings.hub.dataload.uploader as uploader

class PharosUploader(uploader.DummySourceUploader):
    name = "pharos"

    @classmethod
    def get_mapping(self):
        mapping = {
            "pharos": {
                "properties": {
                    "target_id":  {"type": "integer"}
                }
            }
        }
        return mapping
github biothings / mychem.info / src / hub / dataload / sources / drugcentral / drugcentral_upload.py View on Github external
import biothings.hub.dataload.uploader as uploader

class DrugCentralUploader(uploader.DummySourceUploader):

    name = "drugcentral"
    __metadata__ = {
            "src_meta" : {
                "url" : "http://drugcentral.org/",
                "license_url" : "http://drugcentral.org/privacy",
                "license_url_short" : "http://bit.ly/2SeEhUy",
                "license" : "CC BY-SA 4.0",
                }
            }

    @classmethod
    def get_mapping(klass):
        mapping = {
                "drugcentral": {
                    "properties": {