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_BuildDoc.parse_backend()
Involved class: from biothings.hub.dataindex.indexer import _BuildDoc
from biothings.hub.dataindex.indexer import _BuildDoc
A sample input document from myvariant_hubdb.src_build is as below:
myvariant_hubdb.src_build
{ _id : "yy_test_superhot_hg19_20220628_maatbmxp" target_backend : "mongo" target_name : "yy_test_superhot_hg19_20220628_maatbmxp" backend_url : "yy_test_superhot_hg19_20220628_maatbmxp" # other fields omitted }
With the above argument, _BuildDoc.parse_backend() will return the following backend:
_BuildBackend(host=..., port=..., dbs="myvariant", col="yy_test_superhot_hg19_20220628_maatbmxp")
while the correct backend should be:
_BuildBackend(host=..., port=..., dbs="myvariant_hubdb", col="src_build")
target_name
backend_url
src_build
Use from biothings.utils.hub_db import get_src_build to locate the myvariant_hubdb.src_build collection for now, at least in MyVariant hub.
from biothings.utils.hub_db import get_src_build
The text was updated successfully, but these errors were encountered:
erikyao
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Description
Involved class:
from biothings.hub.dataindex.indexer import _BuildDoc
A sample input document from
myvariant_hubdb.src_build
is as below:With the above argument,
_BuildDoc.parse_backend()
will return the following backend:while the correct backend should be:
Hypothesis
_BuildDoc.parse_backend()
is wrong, ortarget_name
andbackend_url
are not correctly written for MyVariantsrc_build
docs, and thus cause_BuildDoc.parse_backend()
to output wrong backends.Workaround
Use
from biothings.utils.hub_db import get_src_build
to locate themyvariant_hubdb.src_build
collection for now, at least in MyVariant hub.The text was updated successfully, but these errors were encountered: