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request_osr_getBloodTestComponentAverage.json
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request_osr_getBloodTestComponentAverage.json
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[{
"blueprint": {
"INTERNAL_STRUCTURE": {
"Overview": {
"name": "osr_hospital_vdc",
"description": "This VDC provides information about biographical data and blood tests of the patients of Ospedale San Raffaele in Milan",
"tags": [{
"method_id": "getPatientBiographicalData",
"tags": [
"OSR",
"patient",
"hospital",
"biographical",
"profile"
]
},
{
"method_id": "getLastValuesForBloodTest",
"tags": [
"OSR",
"patient",
"hospital",
"blood",
"test"
]
},
{
"method_id": "getAllValuesForBloodTestComponent",
"tags": [
"OSR",
"patient",
"hospital",
"blood",
"test",
"component"
]
},
{
"method_id": "getBloodTestComponentAverage",
"tags": [
"OSR",
"patient",
"hospital",
"blood",
"test",
"component",
"age-range",
"research",
"pseudonymization",
"anonymization",
"GDPR-compliance"
]
}
]
},
"Data_Sources": [{
"id": "bloodTestSource",
"description": "Minio source containing blood tests for the hospital patients",
"class": "object storage",
"type": "Minio",
"parameters": {
"spark_hadoop_fs_s3a_endpoint": "http://MINIO:9000",
"spark_hadoop_fs_s3a_access_key": "ACCESS_KEY",
"spark_hadoop_fs_s3a_secret_key": "SECRET_KEY",
"spark_hadoop_fs_s3a_path_style_access": "true",
"spark_hadoop_fs_s3a_impl": "org.apache.hadoop.fs.s3a.S3AFileSystem",
"s3_filename": "s3a://ditas.ehealth-sample/ditas-blood-tests.parquet"
},
"schema": {}
},
{
"id": "patientBiographicalData",
"description": "Relational database containing biographical data for the hospital patients",
"class": "relational database",
"type": "MySQL",
"parameters": {
"ip": "BIO_HOST",
"port": "3306",
"user": "BIO_USER",
"password": "BIO_PASSWORD"
},
"schema": {
"type": "object",
"properties": {
"addressCity": {
"type": "string"
},
"addressRoad": {
"type": "string"
},
"addressRoadNumber": {
"type": "integer"
},
"addressPostalCode": {
"type": "integer"
},
"addressTelephoneNumber": {
"type": "integer"
},
"birthCity": {
"type": "string"
},
"nationality": {
"type": "string"
},
"job": {
"type": "string"
},
"schoolYears": {
"type": "integer"
},
"birthDate": {
"type": "date"
},
"gender": {
"type": "string"
},
"name": {
"type": "string"
},
"patientId": {
"type": "string"
},
"socialId": {
"type": "string"
},
"surname": {
"type": "string"
},
"familyDoctorId": {
"type": "string"
}
}
}
}
],
"Flow": {
"platform": "Spark",
"parameters": {
"spark_master": "spark://SPARK:7077",
"spark_app_name": "PatientBloodTestsVDC",
"spark_jars": "mysql-connector-java-5.1.45/mysql-connector-java-5.1.45-bin.jar,hadoop-aws-3.0.0.jar,aws-java-sdk-bundle-1.11.271.jar"
}
},
"Testing_Output_Data": [{
"method_id": "getPatientBiographicalData",
"zip_data": "http://localhost:8080"
},
{
"method_id": "getLastValuesForBloodTest",
"zip_data": "http://localhost:8080"
},
{
"method_id": "getAllValuesForBloodTestComponent",
"zip_data": "http://localhost:8080"
},
{
"method_id": "getBloodTestComponentAverage",
"zip_data": "http://localhost:8080"
}
]
},
"DATA_MANAGEMENT": [{
"method_id": "getPatientBiographicalData",
"attributes": {
"dataUtility": [{
"id": "availability_90",
"description": "Availability 90",
"type": "Availability",
"properties": {
"availability": {
"unit": "percentage",
"minimum": 90
}
}
},
{
"id": "responseTime_1",
"description": "ResponseTime 1",
"type": "ResponseTime",
"properties": {
"responseTime": {
"maximum": 1,
"unit": "second"
}
}
},
{
"id": "timeliness_06",
"description": "Timeliness 0.6",
"type": "Timeliness",
"properties": {
"timeliness": {
"maximum": 0.6,
"unit": "NONE"
}
}
}
],
"security": [{
"id": "encryption_AES128",
"description": "Encryption AES 128",
"type": "TransportEncryption",
"properties": {
"protocol": {
"unit": "enum",
"value": "TLS"
},
"algorithm": {
"unit": "enum",
"value": "AES"
},
"keyLength": {
"unit": "number",
"value": 128
}
}
},
{
"id": "tracing_1",
"description": "Tracing 1",
"type": "Tracing",
"properties": {
"level": {
"unit": "enum",
"value": "datasource"
},
"sampleRate": {
"unit": "percentage",
"value": 1
},
"instrumentation": {
"unit": "enum",
"value": "VDC"
}
}
},
{
"id": "acl_userPW_doctor",
"description": "ACL username/password doctor_er_id",
"type": "ACL",
"properties": {
"protocol": {
"unit": "enum",
"value": "username/password"
},
"credentials": {
"unit": "list",
"value": [
"doctor_er_id"
]
}
}
}
],
"privacy": []
}
},
{
"method_id": "getLastValuesForBloodTest",
"attributes": {
"dataUtility": [{
"id": "availability_90",
"description": "Availability 90",
"type": "Availability",
"properties": {
"availability": {
"unit": "percentage",
"minimum": 90
}
}
},
{
"id": "responseTime_1",
"description": "ResponseTime 1",
"type": "ResponseTime",
"properties": {
"responseTime": {
"maximum": 1,
"unit": "second"
}
}
},
{
"id": "timeliness_06",
"description": "Timeliness 0.6",
"type": "Timeliness",
"properties": {
"timeliness": {
"maximum": 0.6,
"unit": "NONE"
}
}
}
],
"security": [{
"id": "encryption_AES128",
"description": "Encryption AES 128",
"type": "TransportEncryption",
"properties": {
"protocol": {
"unit": "enum",
"value": "TLS"
},
"algorithm": {
"unit": "enum",
"value": "AES"
},
"keyLength": {
"unit": "number",
"value": 128
}
}
},
{
"id": "tracing_1",
"description": "Tracing 1",
"type": "Tracing",
"properties": {
"level": {
"unit": "enum",
"value": "datasource"
},
"sampleRate": {
"unit": "percentage",
"value": 1
},
"instrumentation": {
"unit": "enum",
"value": "VDC"
}
}
},
{
"id": "acl_userPW_doctor",
"description": "ACL username/password doctor_er_id",
"type": "ACL",
"properties": {
"protocol": {
"unit": "enum",
"value": "username/password"
},
"credentials": {
"unit": "list",
"value": [
"doctor_er_id"
]
}
}
}
],
"privacy": []
}
},
{
"method_id": "getAllValuesForBloodTestComponent",
"attributes": {
"dataUtility": [{
"id": "availability_90",
"description": "Availability 90",
"type": "Availability",
"properties": {
"availability": {
"unit": "percentage",
"minimum": 90
}
}
},
{
"id": "responseTime_1",
"description": "ResponseTime 1",
"type": "ResponseTime",
"properties": {
"responseTime": {
"maximum": 1,
"unit": "second"
}
}
},
{
"id": "timeliness_06",
"description": "Timeliness 0.6",
"type": "Timeliness",
"properties": {
"timeliness": {
"maximum": 0.6,
"unit": "NONE"
}
}
}
],
"security": [{
"id": "encryption_AES128",
"description": "Encryption AES 128",
"type": "TransportEncryption",
"properties": {
"protocol": {
"unit": "enum",
"value": "TLS"
},
"algorithm": {
"unit": "enum",
"value": "AES"
},
"keyLength": {
"unit": "number",
"value": 128
}
}
},
{
"id": "tracing_1",
"description": "Tracing 1",
"type": "Tracing",
"properties": {
"level": {
"unit": "enum",
"value": "datasource"
},
"sampleRate": {
"unit": "percentage",
"value": 1
},
"instrumentation": {
"unit": "enum",
"value": "VDC"
}
}
},
{
"id": "acl_userPW_doctor",
"description": "ACL username/password doctor_er_id",
"type": "ACL",
"properties": {
"protocol": {
"unit": "enum",
"value": "username/password"
},
"credentials": {
"unit": "list",
"value": [
"doctor_er_id"
]
}
}
}
],
"privacy": []
}
},
{
"method_id": "getBloodTestComponentAverage",
"attributes": {
"dataUtility": [{
"id": "volume_9500",
"description": "volume 9500",
"type": "Volume",
"properties": {
"volume": {
"value": 9500,
"unit": "tuple"
}
}
},
{
"id": "accuracy_07",
"description": "Accuracy",
"type": "Accuracy",
"properties": {
"accuracy": {
"minimum": 0.7,
"unit": "none"
}
}
},
{
"id": "processCompleteness_8",
"description": "Process completeness 8",
"type": "Process completeness",
"properties": {
"completeness": {
"minimum": 8,
"unit": "percentage"
}
}
},
{
"id": "scaleUpMemory",
"description": "scale-up memory",
"type": "Scale-up",
"properties": {
"ramGain": {
"unit": "percentage",
"value": 150
},
"ramLimit": {
"unit": "percentage",
"value": 99
}
}
},
{
"id": "scaleUpSpace",
"description": "scale-up space",
"type": "Scale-up",
"properties": {
"spaceGain": {
"unit": "percentage",
"value": 150
},
"spaceLimit": {
"unit": "percentage",
"value": 99
}
}
}
],
"security": [{
"id": "encryption_AES128",
"description": "Encryption AES 128",
"type": "TransportEncryption",
"properties": {
"protocol": {
"unit": "enum",
"value": "TLS"
},
"algorithm": {
"unit": "enum",
"value": "AES"
},
"keyLength": {
"unit": "number",
"value": 128
}
}
},
{
"id": "tracing_1",
"description": "Tracing 1",
"type": "Tracing",
"properties": {
"level": {
"unit": "enum",
"value": "datasource"
},
"sampleRate": {
"unit": "percentage",
"value": 1
},
"instrumentation": {
"unit": "enum",
"value": "VDC"
}
}
},
{
"id": "acl_userPW_researcher",
"description": "ACL username/password researcher_id",
"type": "ACL",
"properties": {
"protocol": {
"unit": "enum",
"value": "username/password"
},
"credentials": {
"unit": "list",
"value": [
"researcher_id"
]
}
}
}
],
"privacy": [{
"id": "purposeControl_research",
"description": "PurposeControl research",
"type": "PurposeControl",
"properties": {
"availablePurpose": {
"unit": "list",
"value": [
"research",
"medical research",
"nutritional research"
]
},
"allowedGuarantor": {
"unit": "list",
"value": [
"d63d0e21fdc05f618d55ef306c54af82"
]
}
}
}]
}
}
],
"ABSTRACT_PROPERTIES": [],
"COOKBOOK_APPENDIX": {},
"EXPOSED_API": {
"openapi": "3.0.1",
"info": {
"title": "CAF API",
"version": "0.0.1"
},
"paths": {
"/patient/{SSN}": {
"get": {
"summary": "Get patient's biographical data",
"description": "This method returns the biographical data for the specified patient (identified via SSN), to be used by medical doctors",
"operationId": "getPatientBiographicalData",
"parameters": [{
"name": "SSN",
"in": "path",
"description": "SSN of the patient",
"required": true,
"schema": {
"type": "string"
}
}],
"responses": {
"200": {
"description": "Biographical data of the patient",
"content": {
"application/json": {
"schema": {
"type": "object",
"properties": {
"SSN": {
"type": "string"
},
"name": {
"type": "string"
},
"surname": {
"type": "string"
},
"gender": {
"type": "string"
},
"birthDate": {
"type": "string"
},
"addressCity": {
"type": "string"
},
"addressRoad": {
"type": "string"
},
"addressRoadNumber": {
"type": "integer"
},
"addressPostalCode": {
"type": "integer"
},
"telephoneNumber": {
"type": "integer"
},
"birthCity": {
"type": "string"
},
"nationality": {
"type": "string"
},
"job": {
"type": "string"
},
"schoolYears": {
"type": "integer"
},
"familyDoctorId": {
"type": "string"
},
"_links": {
"type": "object",
"properties": {
"self": {
"type": "object",
"properties": {
"href": {
"type": "string"
}
},
"required": [
"href"
]
},
"blood-test-summary": {
"type": "object",
"properties": {
"href": {
"type": "string"
}
},
"required": [
"href"
]
}
},
"required": [
"self",
"blood-test-summary"
]
}
},
"required": [
"patientId",
"SSN",
"name",
"surname",
"gender",
"birthDate",
"addressCity",
"addressRoad",
"addressRoadNumber",
"addressPostalCode",
"telephoneNumber",
"birthCity",
"nationality",
"job",
"schoolYears",
"familyDoctorId",
"_links"
]
}
}
}
},
"404": {
"description": "Patient not found"
}
},
"x-data-sources": [
"patientBiographicalData"
]
}
},
"/patient/{SSN}/blood-test/summary": {
"get": {
"summary": "Get patient's latest values for all measured components",
"description": "This method returns the latest values of all the blood test components measured on a patient (identified by his SSN), to be used by medical doctors",
"operationId": "getLastValuesForBloodTest",
"parameters": [{
"name": "SSN",
"in": "path",
"description": "SSN of the patient",
"required": true,
"schema": {
"type": "string"
}
}],
"responses": {
"200": {
"description": "Latest values of all blood test components measured on the patient",
"content": {
"application/json": {
"schema": {
"type": "object",
"properties": {
"components": {
"type": "array",
"items": {
"type": "object",
"properties": {
"date": {
"type": "string"
},
"name": {
"type": "string"
},
"value": {
"type": "object"
}
},
"required": [
"date",
"name",
"value"
]
}
},
"_links": {
"type": "object",
"properties": {
"self": {
"type": "object",
"properties": {
"href": {
"type": "string"
}
},
"required": [
"href"
]
},
"patient": {
"type": "object",
"properties": {
"href": {
"type": "string"
}
},
"required": [
"href"
]
},
"timeseries": {
"type": "object",
"properties": {
"templated": {
"type": "boolean",
"default": true
},
"href": {
"type": "string",
"default": "/patient/some-SSN/blood-test/component/{name}"
}
},
"required": [
"href",
"templated"
]
}
},
"required": [
"self",
"patient",
"timeseries"
]
}
},
"required": [
"components",
"_links"
]
}
}
}
},
"404": {
"description": "Patient not found"
}
},
"x-data-sources": [
"bloodTestSource",
"patientBiographicalData"
]
}
},
"/patient/{SSN}/blood-test/component/{component}": {
"get": {
"summary": "Get timeseries of patient's blood test component",
"description": "This method returns the collected values for a specific blood test component of a patient (identified by his SSN), to be used by medical doctors",
"operationId": "getAllValuesForBloodTestComponent",
"parameters": [{
"name": "SSN",
"in": "path",
"description": "SSN of the patient",
"required": true,
"schema": {
"type": "string"
}
},
{
"name": "component",
"in": "path",
"description": "Blood test component for which the values are requested",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Values for the specified blood test component in the patient's blood tests",
"content": {
"application/json": {
"schema": {
"type": "object",
"properties": {
"series": {
"type": "array",
"items": {
"type": "object",
"properties": {
"date": {
"type": "string"
},
"value": {
"type": "object"
}
},
"required": [
"date",
"value"
]
}
},
"_links": {
"type": "object",
"properties": {
"self": {
"type": "object",
"properties": {
"href": {
"type": "string"
}
},
"required": [
"href"
]
},
"patient": {
"type": "object",
"properties": {
"href": {
"type": "string"
}
},
"required": [
"href"
]
}
},
"required": [
"self",
"patient"
]
}
},
"required": [
"series",
"_links"
]
}
}
}
},
"404": {
"description": "Patient not found"
}
},
"x-data-sources": [
"bloodTestSource",
"patientBiographicalData"
]
}
},
"/blood-test/component/{component}/average/{startAgeRange}-{endAgeRange}": {
"get": {
"summary": "Get average of component over an age range",
"description": "This method returns the average value for a specific blood test component in a specific age range, to be used by researchers. Since data are for researchers, patients' identifiers and quasi-identifiers won't be returned, making the output of this method anonymized.",
"operationId": "getBloodTestComponentAverage",
"parameters": [{
"name": "component",
"in": "path",
"description": "Blood test component for which the last value is requested",
"required": true,
"schema": {
"type": "string"
}
},
{
"name": "startAgeRange",
"in": "path",
"description": "Start age in age range",
"required": true,
"schema": {
"type": "number"
}
},
{
"name": "endAgeRange",
"in": "path",
"description": "End age in age range",
"required": true,
"schema": {
"type": "number"
}
}
],
"responses": {
"200": {
"description": "Average value for the specified component in the selected age range",
"content": {
"application/json": {
"schema": {
"type": "object",
"properties": {
"value": {
"type": "number"
},
"_links": {
"type": "object",
"properties": {
"self": {
"type": "object",
"properties": {
"href": {