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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'],
}
}
}
}
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'],
}
}
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)
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 = {
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 = {
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"
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
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):
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
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": {