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querySelection.py
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querySelection.py
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import triplestoreConection
import chevron
from perseo.main import milisec
import sys
import os
class QueryBuilder:
TRIPLE_STORE_CONECTION = triplestoreConection.TripleStoreConection()
# FILTER_SEX= "True"
# FILTER_DISEASE= "True"
# FILTER_SYMPTOM= "True"
# FILTER_GENE_VARIANT= "True"
# FILTER_BIRTHYEAR= "True"
# FILTER_AGE_SYMPTOM_ONSET= "True"
# FILTER_AGE_DIAGNOSIS= "True"
FILTER_SEX = os.getenv("FILTER_SEX")
FILTER_DISEASE = os.getenv("FILTER_DISEASE")
FILTER_SYMPTOM = os.getenv("FILTER_SYMPTOM")
FILTER_GENE_VARIANT = os.getenv("FILTER_GENE_VARIANT")
FILTER_BIRTHYEAR = os.getenv("FILTER_BIRTHYEAR")
FILTER_AGE_SYMPTOM_ONSET = os.getenv("FILTER_AGE_SYMPTOM_ONSET")
FILTER_AGE_DIAGNOSIS = os.getenv("FILTER_AGE_DIAGNOSIS")
def filtering_CURIE(self):
permitted_terms = []
curie_formats = []
obo_curie_format={
"id": "ncit",
"name": "NCIT",
"url": "http://purl.obolibrary.org/obo/ncit.owl",
"version": "2023-101-19",
"namespacePrefix": "obo",
"iriPrefix": "http://purl.obolibrary.org/obo/"
}
curie_formats.append(obo_curie_format)
if self.FILTER_SEX == "True":
sex_resource={
"id": "ncit:C28421",
"label": "Sex",
"type": "ontology",
"scopes": [
"individuals"
]
}
permitted_terms.append(sex_resource)
if self.FILTER_DISEASE == "True":
disease_resource={
"id": "ncit:C2991",
"label": "Disease or Disorder",
"type": "ontology",
"scopes": [
"individuals"
]
}
permitted_terms.append(disease_resource)
ordo_curie={
"id": "ordo",
"name": "Orphanet Ontology",
"url": "https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl",
"version": "4.4",
"namespacePrefix": "ordo",
"iriPrefix": "http://www.orpha.net/ORDO/"
}
curie_formats.append(ordo_curie)
if self.FILTER_SYMPTOM == "True":
phenotype_resource={
"id": "sio:SIO_010056",
"label": "Phenotype",
"type": "ontology",
"scopes": [
"individuals"
]
}
permitted_terms.append(phenotype_resource)
hpo_curie={
"id": "hp",
"name": "Human Phenotype Ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2024-07-01",
"namespacePrefix": "hp",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
curie_formats.append(hpo_curie)
sio_curie={
"id": "sio",
"name": "Semanticscience Integrated Ontology",
"url": "http://semanticscience.org/ontology/sio/v1.59/sio-release.owl",
"version": "1.59",
"namespacePrefix": "sio",
"iriPrefix": "http://semanticscience.org/resource/"
}
curie_formats.append(sio_curie)
if self.FILTER_GENE_VARIANT == "True":
genotype_resource={
"id": "edam:data_2295",
"label": "Causative Genes",
"type": "alphanumerical",
"scopes": [
"individuals"
]
}
permitted_terms.append(genotype_resource)
edam_curie={
"id": "edam",
"name": "EDAM",
"url": "https://edamontology.org/EDAM_1.25.owl",
"version": "1.21",
"namespacePrefix": "edam",
"iriPrefix": "http://edamontology.org/"
}
curie_formats.append(edam_curie)
if self.FILTER_BIRTHYEAR == "True":
birthyear_resource={
"id": "ncit:C83164",
"label": "Age this year",
"type": "numeric",
"scopes": [
"individuals"
]
}
permitted_terms.append(birthyear_resource)
if self.FILTER_AGE_SYMPTOM_ONSET == "True":
symptom_onset_resource={
"id": "ncit:C124353",
"label": "Age at symptom onset",
"type": "numeric",
"scopes": [
"individuals"
]
}
permitted_terms.append(symptom_onset_resource)
if self.FILTER_AGE_DIAGNOSIS == "True":
age_diagnosis_onset_resource={
"id": "ncit:C156420",
"label": "Age at diagnosis",
"type": "numeric",
"scopes": [
"individuals"
]
}
permitted_terms.append(age_diagnosis_onset_resource)
return permitted_terms, curie_formats
def detect_number_type(self, string):
try:
# Try converting to integer
int_value = int(string)
return int_value
except ValueError:
sys.exit("You can't add non numerical nor fractional years to the filters related to Age, like AGE OF SYMPTOM ONSET and AGE OF DIAGNOSIS")
def curate_values(self, values, tag):
if tag == "ont":
if isinstance(values, str):
curated_values = values
elif isinstance(values, list):
curated_values = [f"{value} " for value in values]
elif tag == "lit":
if isinstance(values, str):
curated_values = [f"'{values}'"]
elif isinstance(values, list):
curated_values = [f"'{value}'" for value in values]
else:
sys.exit("No tag assigned.")
return " ".join(curated_values)
def individuals_query_builder(self, input_data):
with open('templates/block1_SELECT.mustache', 'r') as f:
queryText = chevron.render(f)
if input_data.query.filters:
list_filters_used = []
symp_info = {}
onset_info = {}
# Store parameter.types to for later validation
for parameter in input_data.query.filters:
if parameter.type:
list_filters_used += [parameter.type]
for parameter in input_data.query.filters:
if parameter.type:
# SEX FILTER
if parameter.type == "obo:NCIT_C28421" or parameter.type =="http://purl.obolibrary.org/obo/NCIT_C28421":
if self.FILTER_SEX == "True":
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': parameter.operator,
'attribute':parameter.id,
'operator_output': "=",
'output': "obo:NCIT_C160908",
'cde':"sex"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"sex"})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, filter for SEX is not available")
# DISEASE FILTER
elif parameter.type == "obo:NCIT_C2991" or parameter.type == "http://purl.obolibrary.org/obo/NCIT_C2991":
if self.FILTER_DISEASE == "True":
stamp = "disease" + milisec()
if isinstance(parameter.id, str):
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': parameter.operator,
'attribute':parameter.id,
'operator_output': "=",
'output': "obo:NCIT_C154625",
'cde':stamp})
queryText = queryText + Block
elif isinstance(parameter.id, list):
curated_values = self.curate_values(parameter.id, tag="ont")
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "!=",
'attribute': "sio:SIO_000614",
'operator_output': "=",
'output': "obo:NCIT_C154625",
'cde':stamp})
queryText = queryText + Block
with open('templates/block4_VALUES.mustache', 'r') as f:
Block = chevron.render(f, {
'instance': "attribute_type",
'values': curated_values,
'cde':stamp})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':stamp})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, filter for DISEASE is not available")
# PHENOTYPE FILTER
elif ("sio:SIO_010056" in list_filters_used or "http://semanticscience.org/resource/SIO_010056" in list_filters_used) and ("obo:NCIT_C124353" not in list_filters_used and "http://purl.obolibrary.org/obo/NCIT_C124353" not in list_filters_used):
if self.FILTER_SYMPTOM == "True":
stamp = "phenotype" + milisec()
if isinstance(parameter.id, str):
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': parameter.operator,
'attribute': parameter.id,
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':stamp})
queryText = queryText + Block
elif isinstance(parameter.id, list):
curated_values = self.curate_values(parameter.id, tag="ont")
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "!=",
'attribute': "sio:SIO_000614",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':stamp})
queryText = queryText + Block
with open('templates/block4_VALUES.mustache', 'r') as f:
Block = chevron.render(f, {
'instance': "attribute_type",
'values': curated_values,
'cde':stamp})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':stamp})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, filter for SYMPTOM/PHENOTYPE is not available")
# GENOTYPE FILTER
elif parameter.type == "edam:data_2295":
if self.FILTER_GENE_VARIANT == "True":
stamp = "genotype" + milisec()
if isinstance(parameter.id, str):
curated_values = self.curate_values(parameter.id, tag="lit")
with open('templates/block4_VALUES.mustache', 'r') as f:
Block = chevron.render(f, {
'instance': "value",
'values': curated_values,
'cde':stamp})
queryText = queryText + Block
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "obo:NCIT_C15709",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "sio:SIO_000614",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':stamp})
queryText = queryText + Block
with open('templates/block2b_OUTPUT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':stamp})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':stamp})
queryText = queryText + Block
elif isinstance(parameter.id, list):
curated_values = self.curate_values(parameter.id, tag="lit")
with open('templates/block4_VALUES.mustache', 'r') as f:
Block = chevron.render(f, {
'instance': "attribute_type",
'values': curated_values,
'cde':stamp})
queryText = queryText + Block
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "obo:NCIT_C15709",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "sio:SIO_000614",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':stamp})
queryText = queryText + Block
with open('templates/block2b_OUTPUT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':stamp})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':stamp})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, filter for GENETIC VARIANT is not available")
# BIRTHYEAR FILTER
elif parameter.type == "obo:NCIT_C83164" or parameter.type == "http://purl.obolibrary.org/obo/NCIT_C83164":
if self.FILTER_BIRTHYEAR == "True":
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': parameter.type,
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':"birthyear"})
queryText = queryText + Block
with open('templates/block3b_OUTPUT_VALUE.mustache', 'r') as f:
Block = chevron.render(f, {'value': parameter.id, 'operator': parameter.operator, 'datatype':"xsd:integer", 'cde':"birthyear"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"birthyear"})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, filter for BIRTHYEAR is not available")
# AGE_OF_SYMPTOM FILTER
elif ("sio:SIO_010056" not in list_filters_used and "http://semanticscience.org/resource/SIO_010056" not in list_filters_used) and ("obo:NCIT_C124353" in list_filters_used or "http://purl.obolibrary.org/obo/NCIT_C124353" in list_filters_used):
if self.FILTER_AGE_SYMPTOM_ONSET == "True":
parameter_checked = self.detect_number_type(parameter.id)
with open('templates/block1b_BIND.mustache', 'r') as f:
Block = chevron.render(f, {'value': parameter_checked, 'operator': parameter.operator ,'st':"s_",'cde':"s_onset", "cde2":"s_birthdate"})
queryText = queryText + Block
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "obo:NCIT_C68615",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':"s_birthdate"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_birthdate"})
queryText = queryText + Block
with open('templates/block5b_CONTEXT_DATE.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_birthdate"})
queryText = queryText + Block
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "obo:NCIT_C124353",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':"s_onset"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_onset"})
queryText = queryText + Block
with open('templates/block5b_CONTEXT_DATE.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_onset"})
queryText = queryText + Block
with open('templates/block6_CLOSE.mustache', 'r') as f:
Block = chevron.render(f, {})
queryText = queryText + Block
with open('templates/block6_CLOSE.mustache', 'r') as f:
Block = chevron.render(f, {})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, filter for AGE OF SYMPTOM ONSET is not available")
# AGE_AT_DIAGNOSIS FILTER
elif parameter.type == "obo:NCIT_C156420" or parameter.type == "http://purl.obolibrary.org/obo/NCIT_C156420":
if self.FILTER_AGE_DIAGNOSIS == "True":
parameter_checked = self.detect_number_type(parameter.id)
with open('templates/block1b_BIND.mustache', 'r') as f:
Block = chevron.render(f, {'value': parameter_checked, 'operator': parameter.operator ,'st':"d_",'cde':"d_onset", "cde2":"d_birthdate"})
queryText = queryText + Block
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "obo:NCIT_C68615",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':"d_birthdate"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"d_birthdate"})
queryText = queryText + Block
with open('templates/block5b_CONTEXT_DATE.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"d_birthdate"})
queryText = queryText + Block
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "sio:SIO_000614",
'operator_output': "=",
'output': "obo:NCIT_C154625",
'cde':"d_onset"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"d_onset"})
queryText = queryText + Block
with open('templates/block5b_CONTEXT_DATE.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"d_onset"})
queryText = queryText + Block
with open('templates/block6_CLOSE.mustache', 'r') as f:
Block = chevron.render(f, {})
queryText = queryText + Block
with open('templates/block6_CLOSE.mustache', 'r') as f:
Block = chevron.render(f, {})
queryText = queryText + Block
else:
sys.exit("You have used unpermitted filter for this repository, filter for AGE OF DIAGNOSIS is not available")
else:
# DISEASE FILTER
if self.FILTER_DISEASE == "True":
if self.FILTER_DISEASE == "True":
stamp = "disease" + milisec()
if isinstance(parameter.id, str):
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute':parameter.id,
'operator_output': "=",
'output': "obo:NCIT_C154625",
'cde':stamp})
queryText = queryText + Block
elif isinstance(parameter.id, list):
curated_values = self.curate_values(parameter.id, tag="ont")
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "!=",
'attribute': "sio:SIO_000614",
'operator_output': "=",
'output': "obo:NCIT_C154625",
'cde':stamp})
queryText = queryText + Block
with open('templates/block4_VALUES.mustache', 'r') as f:
Block = chevron.render(f, {
'instance': "attribute_type",
'values': curated_values,
'cde':stamp})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':stamp})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, filter for DISEASE is not available")
# SYMPTOM + SYMPTOM ONSET FILTER
if ("sio:SIO_010056" in list_filters_used or "http://semanticscience.org/resource/SIO_010056" in list_filters_used) and ("obo:NCIT_C124353" in list_filters_used or "http://purl.obolibrary.org/obo/NCIT_C124353" in list_filters_used):
if (self.FILTER_SYMPTOM == "True") and (self.FILTER_AGE_SYMPTOM_ONSET == "True"):
for parameter in input_data.query.filters:
if parameter.type =="sio:SIO_010056" or parameter.type =="http://semanticscience.org/resource/SIO_010056":
symp_info = parameter
elif parameter.type == "obo:NCIT_C124353" or parameter.type =="http://purl.obolibrary.org/obo/NCIT_C124353":
onset_info = parameter
parameter_checked = self.detect_number_type(onset_info.id)
# SYMPTOM + SYMPTOM ONSET FILTER
with open('templates/block1b_BIND.mustache', 'r') as f:
Block = chevron.render(f, {'value': onset_info.id, 'operator': onset_info.operator , 'st':"s_", 'cde':"s_onset", "cde2":"s_birthdate"})
queryText = queryText + Block
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "obo:NCIT_C68615",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':"s_birthdate"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_birthdate"})
queryText = queryText + Block
with open('templates/block5b_CONTEXT_DATE.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_birthdate"})
queryText = queryText + Block
if isinstance(symp_info.id, str):
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': symp_info.operator,
'target': symp_info.id,
'operator_attribute': "=",
'attribute': "obo:NCIT_C124353",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':"s_onset"})
queryText = queryText + Block
elif isinstance(symp_info.id, list):
curated_values = self.curate_values(symp_info.id)
with open('templates/block2_GENERAL.mustache', 'r') as f:
Block = chevron.render(f, {
'process': "sio:SIO_000006",
'operator_target': "!=",
'target': "sio:SIO_000015",
'operator_attribute': "=",
'attribute': "obo:NCIT_C124353",
'operator_output': "=",
'output': "sio:SIO_000015",
'cde':"s_onset"})
queryText = queryText + Block
with open('templates/block4_VALUES.mustache', 'r') as f:
Block = chevron.render(f, {
'instance': "target_type",
'values': curated_values,
'cde':"s_onset"})
queryText = queryText + Block
with open('templates/block5_CONTEXT.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_onset"})
queryText = queryText + Block
with open('templates/block5b_CONTEXT_DATE.mustache', 'r') as f:
Block = chevron.render(f, {'cde':"s_onset"})
queryText = queryText + Block
with open('templates/block6_CLOSE.mustache', 'r') as f:
Block = chevron.render(f, {})
queryText = queryText + Block
with open('templates/block6_CLOSE.mustache', 'r') as f:
Block = chevron.render(f, {})
queryText = queryText + Block
else:
sys.exit( "You have used unpermitted filter for this repository, neither SYMPTOM nor AGE OF SYMPTOM ONSET is available")
with open('templates/block6_CLOSE.mustache', 'r') as f:
Block = chevron.render(f, {})
queryText = queryText + Block
else:
sys.exit("Any of the parameters you passed is not corrected, please check you input JSON request body")
# stamp_file = "file" + milisec() + ".ttl"
# f = open(stamp_file, "a")
# f.write(queryText)
# f.close()
result = self.TRIPLE_STORE_CONECTION.get_count_individuals(queryText)
count = result["results"]["bindings"][0]["count"]["value"]
return count