def get_facets(solr_api_url,solr_api_key,q=query,fields=["document_uuid_s","guidance_s","effectendpoint_s"]):
config,config_servers, config_security, auth_object, msg = aa.parseOpenAPI3()
if auth_object!=None:
auth_object.setKey(solr_api_key)
facets = client_solr.Facets()
facets.set_annotation_folder(annotation_folder)
return facets.summary(solr_api_url,auth_object, query=q,fields=fields)
def retrieve_params(solr_api_url, solr_api_key):
config, config_servers, config_security, auth_object, msg = aa.parseOpenAPI3(
)
if auth_object != None:
auth_object.setKey(solr_api_key)
r = client_solr.get(solr_api_url,
query={
"q": "*:*",
"wt": "csv",
"rows": 0
},
auth=auth_object)
params = pd.read_csv(io.StringIO(r.content.decode('utf-8')))
tmp = pd.DataFrame(params.columns, columns=["field"])
tmp["type"] = tmp["field"].apply(lambda x: "number" if x.endswith(
"_d") else ("QUALIFIER" if x.endswith("QUALIFIER") else
("unit" if x.endswith("UNIT") else "STRING")))
tmp["field_clean"] = tmp["field"].apply(lambda col: re.sub(
"_s$", "",
re.sub(
"_d$", "",
re.sub(
"_UPQUALIFIER_s$", "",
re.sub(
"_LOVALUE_d$", "",
re.sub(
"_LOQUALIFIER_s$", "",
re.sub("_UPVALUE_d$", "", re.sub("_UNIT_s$", "", col)))
)))).replace(".", "_"))
tmp["title"] = tmp["field_clean"].apply(lambda col: re.sub(
"^T_", "", re.sub("^E_", "", col)).replace("_", " ").strip())
tmp.sort_values(by=['field_clean'], inplace=True)
return tmp
def retrieve_params(solr_api_url,solr_api_key,query="*:*"):
config,config_servers, config_security, auth_object, msg = aa.parseOpenAPI3()
if auth_object!=None:
auth_object.setKey(solr_api_key)
r = client_solr.get(solr_api_url ,query={"q": query, "wt": "json", "rows" : 1000000 , "fq" : "type_s:params"},auth=auth_object)
tmp = pd.DataFrame(r.json()["response"]["docs"])
return tmp
def get_facets(solr_api_url,
solr_api_key,
q="*:*",
fields=[
"document_uuid_s", "topcategory_s", "endpointcategory_s",
"E.method_s"
]):
config, config_servers, config_security, auth_object, msg = aa.parseOpenAPI3(
)
if auth_object != None:
auth_object.setKey(solr_api_key)
facets = client_solr.Facets()
return facets.summary(solr_api_url, auth_object, query=q, fields=fields)
def prepare(solr_api_url,
solr_api_key,
folder_output,
query="owner_name_s:GRACIOUS",
method="BET"):
#print(query)
config, config_servers, config_security, auth_object, msg = aa.parseOpenAPI3(
)
if auth_object != None:
auth_object.setKey(solr_api_key)
q = query
results = get_documents_by_method(solr_api_url, auth_object, q, method)
return results
# + tags=["parameters"]
upstream = None
folder_output = None
solr_api_url = None
solr_api_key = None
annotation_folder = None
query=None
plot_dose_response=None
# -
from pynanomapper import client_solr,aa
import os, os.path
config,config_servers, config_security, auth_object, msg = aa.parseOpenAPI3()
if auth_object!=None:
auth_object.setKey(solr_api_key)
def log_query(q):
#logger.debug(q)
pass
def beautify(r):
pass
# Database records
facets = client_solr.Facets()
facets.set_annotation_folder(annotation_folder)
_query = "*:*" if query=="" else query.replace("owner_name_s","owner_name_hs")
dfm = facets.summary(solr_api_url,auth_object, query=_query,fields=["owner_name_hs"],fq='type_s:substance',log_query=log_query,log_result=beautify)
projects = dfm["owner_name_hs"].unique()