diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 5ab4845eb7a16e26a658180bed9a193b4405fb13..a6a5d65500e624c2b27810043c5cfd0da500a4cc 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -370,6 +370,9 @@ jobs:
- name: Start MONETDB and RABBITMQ containers
run: poetry run inv deploy --no-start-all
+ - name: Load data into DBs
+ run: poetry run inv load-data
+
- name: Start GLOBALNODE container
run: docker run -d --name globalnode -e NODE_IDENTIFIER=globalnode -e NODE_ROLE=GLOBALNODE -e LOG_LEVEL=INFO -e NODE_REGISTRY_IP=172.17.0.1 -e NODE_REGISTRY_PORT=8500 -e RABBITMQ_IP=172.17.0.1 -e RABBITMQ_PORT=5670 -e MONETDB_IP=172.17.0.1 -e MONETDB_PORT=50000 madgik/mipengine_node:latest
@@ -380,10 +383,12 @@ jobs:
run: docker run -d --name localnode2 -e NODE_IDENTIFIER=localnode2 -e NODE_ROLE=LOCALNODE -e LOG_LEVEL=INFO -e NODE_REGISTRY_IP=172.17.0.1 -e NODE_REGISTRY_PORT=8500 -e RABBITMQ_IP=172.17.0.1 -e RABBITMQ_PORT=5672 -e MONETDB_IP=172.17.0.1 -e MONETDB_PORT=50002 madgik/mipengine_node:latest
- name: Start CONTROLLER container
- run: docker run -d --name controller -p 5000:5000 -e NODE_REGISTRY_IP=172.17.0.1 -e NODE_REGISTRY_PORT=8500 madgik/mipengine_controller:latest
+ run: docker run -d --name controller -p 5000:5000 -v $GITHUB_WORKSPACE/tests/demo_data:/opt/data -e CDES_METADATA_PATH=/opt/data -e NODE_REGISTRY_IP=172.17.0.1 -e NODE_REGISTRY_PORT=8500 madgik/mipengine_controller:latest
- - name: Load data into DBs
- run: poetry run inv load-data
+ - name: Wait for services to start
+ uses: jakejarvis/wait-action@master
+ with:
+ time: '20s'
- name: Run e2e tests
run: poetry run pytest tests/e2e_tests
diff --git a/README.md b/README.md
index f5a631024e09818d2587985e6620aad0d5626a51..239643409c8639aaa7f5d6a5e2b6f504bf72ceba 100644
--- a/README.md
+++ b/README.md
@@ -47,6 +47,8 @@
monetdb_image = "madgik/mipenginedb:0.1"
rabbitmq_image = "madgik/mipengine_rabbitmq:0.1"
+ cdes_metadata_path = "./tests/demo_data"
+
node_registry_port = 8500
[[nodes]]
diff --git a/mipengine/common_data_elements.py b/mipengine/common_data_elements.py
index 0edcdfe9a2761b34214db62aafa9a3d4f879f587..4da088f57b1472dc9798b36fa21ac59ce391c899 100644
--- a/mipengine/common_data_elements.py
+++ b/mipengine/common_data_elements.py
@@ -9,7 +9,7 @@ from typing import Set
from dataclasses_json import dataclass_json
-from mipengine.resources import pathologies_metadata
+PATHOLOGY_METADATA_FILENAME = "CDEsMetadata.json"
@dataclass_json
@@ -80,11 +80,24 @@ class CommonDataElement:
class CommonDataElements:
pathologies: Dict[str, Dict[str, CommonDataElement]]
- def __init__(self):
- metadata_path = Path(pathologies_metadata.__file__).parent
-
+ def __init__(self, cdes_metadata_path: str = None):
self.pathologies = {}
- for pathology_metadata_filepath in metadata_path.glob("*.json"):
+
+ if not cdes_metadata_path:
+ return
+
+ cdes_metadata_path = Path(cdes_metadata_path)
+
+ cdes_pathology_metadata_folders = [
+ pathology_folder
+ for pathology_folder in cdes_metadata_path.iterdir()
+ if pathology_folder.is_dir()
+ ]
+
+ for pathology_metadata_folder in cdes_pathology_metadata_folders:
+ pathology_metadata_filepath = (
+ pathology_metadata_folder / PATHOLOGY_METADATA_FILENAME
+ )
try:
pathology_metadata: MetadataGroup = MetadataGroup.from_json(
open(pathology_metadata_filepath).read()
@@ -95,9 +108,12 @@ class CommonDataElements:
for variable in group.variables
}
except Exception as e:
- logging.error(f"Parsing metadata file: {pathology_metadata_filepath}")
+ logging.error(
+ f"Error parsing metadata file: {pathology_metadata_filepath}"
+ )
raise e
- # Adding the subject code cde that doesn't exist in the metadata
+
+ # Adding the subject code cde that doesn't exist in the metadata
self.pathologies[pathology_metadata.code][
"subjectcode"
] = CommonDataElement(
@@ -111,6 +127,3 @@ class CommonDataElements:
max=None,
)
)
-
-
-common_data_elements = CommonDataElements()
diff --git a/mipengine/controller/Dockerfile b/mipengine/controller/Dockerfile
index 6c52ad9481e4540c8b5686b368688af3a928125a..48c8a083b8d3430043743320b6fd27b622929005 100644
--- a/mipengine/controller/Dockerfile
+++ b/mipengine/controller/Dockerfile
@@ -22,6 +22,12 @@ ENV PYTHONUNBUFFERED=1 \
ENV PATH="$POETRY_HOME/bin:$CODE_PATH:$PATH"
WORKDIR $CODE_PATH
+#######################################################
+# Creating the metadata folder
+#######################################################
+ENV CDES_METADATA_PATH="/opt/data"
+RUN mkdir $CDES_METADATA_PATH
+
#######################################################
# Installing poetry and dependencies
#######################################################
diff --git a/mipengine/controller/api/validator.py b/mipengine/controller/api/validator.py
index 8229f83c5270be32d0c9091c351552be9373022c..7318962f09f324b2ede21e78b8af9f2da0b18db3 100644
--- a/mipengine/controller/api/validator.py
+++ b/mipengine/controller/api/validator.py
@@ -10,7 +10,9 @@ from typing import Optional
from mipengine.controller import config as controller_config
from mipengine.common_data_elements import CommonDataElement
-from mipengine.common_data_elements import common_data_elements
+from mipengine.controller.controller_common_data_elements import (
+ controller_common_data_elements,
+)
from mipengine.controller.algorithms_specifications import AlgorithmSpecifications
from mipengine.controller.algorithms_specifications import InputDataStatType
from mipengine.controller.algorithms_specifications import InputDataType
@@ -78,7 +80,7 @@ def _validate_inputdata(
):
_validate_inputdata_pathology_and_dataset(inputdata.pathology, inputdata.datasets)
- _validate_inputdata_filter(inputdata.filters)
+ _validate_inputdata_filter(inputdata.pathology, inputdata.filters)
_validate_algorithm_inputdatas(inputdata, inputdata_specs)
@@ -113,12 +115,17 @@ def _validate_inputdata_pathology_and_dataset(pathology: str, datasets: List[str
)
-def _validate_inputdata_filter(filter):
+def _validate_inputdata_filter(pathology, filter):
"""
Validates that the filter provided have the correct format
following: https://querybuilder.js.org/
"""
- # TODO Add filter
+ # TODO Add filters
+ # validate_proper_filter(
+ # common_data_elements=common_data_elements,
+ # pathology_name=pathology,
+ # rules=filter
+ # )
pass
@@ -177,9 +184,9 @@ def _validate_inputdata_value(
def _get_cde_metadata(cde, pathology):
- pathology_cdes: Dict[str, CommonDataElement] = common_data_elements.pathologies[
- pathology
- ]
+ pathology_cdes: Dict[
+ str, CommonDataElement
+ ] = controller_common_data_elements.pathologies[pathology]
if cde not in pathology_cdes.keys():
raise BadUserInput(
f"The CDE '{cde}' does not exist in pathology '{pathology}'."
diff --git a/mipengine/controller/config.toml b/mipengine/controller/config.toml
index e2932778db68141e35e718df6b3ef5cbad47dcd8..35b0a3371988f9f3f106b9e719f88598f43f9a34 100644
--- a/mipengine/controller/config.toml
+++ b/mipengine/controller/config.toml
@@ -1,4 +1,5 @@
log_level = "INFO"
+cdes_metadata_path = "$CDES_METADATA_PATH"
[node_registry]
ip="$NODE_REGISTRY_IP"
diff --git a/mipengine/controller/controller_common_data_elements.py b/mipengine/controller/controller_common_data_elements.py
new file mode 100644
index 0000000000000000000000000000000000000000..044039f31f3a2afc9479fd51bbd6c0bf31087009
--- /dev/null
+++ b/mipengine/controller/controller_common_data_elements.py
@@ -0,0 +1,6 @@
+from mipengine.common_data_elements import CommonDataElements
+from mipengine.controller import config as controller_config
+
+controller_common_data_elements = CommonDataElements(
+ controller_config.cdes_metadata_path
+)
diff --git a/mipengine/filters.py b/mipengine/filters.py
index 5a68d3d6626b2986a7da90ec9939062cb908300e..90e98e8e965f1219c760aec6df5a9833f4503bde 100644
--- a/mipengine/filters.py
+++ b/mipengine/filters.py
@@ -1,4 +1,4 @@
-from mipengine.common_data_elements import common_data_elements
+from mipengine.common_data_elements import CommonDataElements
from mipengine.datatypes import convert_mip_type_to_python_type
FILTER_OPERATORS = {
@@ -43,7 +43,9 @@ def build_filter_clause(rules):
raise ValueError(f"Filters did not contain the keys: 'condition' or 'id'.")
-def validate_proper_filter(pathology_name: str, rules):
+def validate_proper_filter(
+ common_data_elements: CommonDataElements, pathology_name: str, rules: dict
+):
"""
Validates a given filter in jQuery format.
This function will check the validity of:
@@ -58,19 +60,19 @@ def validate_proper_filter(pathology_name: str, rules):
return
_check_filter_type(rules)
- _check_pathology_exists(pathology_name)
+ _check_pathology_exists(common_data_elements, pathology_name)
if "condition" in rules:
_check_proper_condition(rules["condition"])
rules = rules["rules"]
for rule in rules:
- validate_proper_filter(pathology_name, rule)
+ validate_proper_filter(common_data_elements, pathology_name, rule)
elif "id" in rules:
column_name = rules["id"]
val = rules["value"]
_check_proper_operator(rules["operator"])
- _check_column_exists(pathology_name, column_name)
- _check_value_type(pathology_name, column_name, val)
+ _check_column_exists(common_data_elements, pathology_name, column_name)
+ _check_value_type(common_data_elements, pathology_name, column_name, val)
else:
raise ValueError(
f"Invalid filters format. Filters did not contain the keys: 'condition' or 'id'."
@@ -98,7 +100,7 @@ def _check_proper_operator(operator: str):
raise ValueError(f"Operator: {operator} is not acceptable.")
-def _check_column_exists(pathology_name: str, column: str):
+def _check_column_exists(common_data_elements, pathology_name: str, column: str):
pathology_common_data_elements = common_data_elements.pathologies[pathology_name]
if column not in pathology_common_data_elements.keys():
raise KeyError(
@@ -106,26 +108,31 @@ def _check_column_exists(pathology_name: str, column: str):
)
-def _check_pathology_exists(pathology_name: str):
+def _check_pathology_exists(common_data_elements, pathology_name: str):
if pathology_name not in common_data_elements.pathologies.keys():
raise KeyError(f"Pathology:{pathology_name} does not exist in the metadata!")
-def _check_value_type(pathology_name: str, column: str, value):
+def _check_value_type(common_data_elements, pathology_name: str, column: str, value):
if value is None:
return
if isinstance(value, list):
- [_check_value_type(pathology_name, column, item) for item in value]
+ [
+ _check_value_type(common_data_elements, pathology_name, column, item)
+ for item in value
+ ]
elif isinstance(value, (int, str, float)):
- _check_value_column_same_type(pathology_name, column, value)
+ _check_value_column_same_type(
+ common_data_elements, pathology_name, column, value
+ )
else:
raise TypeError(
f"Value {value} should be of type int, str, float but was {type(value)}"
)
-def _check_value_column_same_type(pathology_name, column, value):
+def _check_value_column_same_type(common_data_elements, pathology_name, column, value):
pathology_common_data_elements = common_data_elements.pathologies[pathology_name]
column_sql_type = pathology_common_data_elements[column].sql_type
if type(value) is not convert_mip_type_to_python_type(column_sql_type):
diff --git a/mipengine/node/config.toml b/mipengine/node/config.toml
index 284c4715fd2af079a3f8f307289bb39a926110c8..d315b2b9cbccb122379b1826dba9d03c90b3bea3 100644
--- a/mipengine/node/config.toml
+++ b/mipengine/node/config.toml
@@ -2,6 +2,8 @@ identifier = "$NODE_IDENTIFIER"
log_level = "$LOG_LEVEL"
role = "$NODE_ROLE"
+cdes_metadata_path = "./tests/demo_data"
+
[node_registry]
ip="$NODE_REGISTRY_IP"
port="$NODE_REGISTRY_PORT"
diff --git a/mipengine/node/monetdb_interface/csv_importer.py b/mipengine/node/monetdb_interface/csv_importer.py
index 4e3e22eebb79a5a5a8da316f30a8c51f8591ca2c..1eabb6b641f41bc41582f3f17ecc7c837a933789 100644
--- a/mipengine/node/monetdb_interface/csv_importer.py
+++ b/mipengine/node/monetdb_interface/csv_importer.py
@@ -17,7 +17,7 @@ from sqlalchemy import null
from sqlalchemy.exc import OperationalError
from mipengine.common_data_elements import CommonDataElement
-from mipengine.common_data_elements import common_data_elements
+from mipengine.common_data_elements import CommonDataElements
from mipengine.node import DATA_TABLE_PRIMARY_KEY
AMOUNT_OF_ROWS_TO_INSERT_INTO_SQL_PER_CALL = 100
@@ -325,6 +325,9 @@ monetdb_password = args.monetdb_password
monetdb_url = args.monetdb_url
monetdb_farm = args.monetdb_farm
+print(f"Importing metadata of pathologies in {data_path}")
+common_data_elements = CommonDataElements(data_path)
+
db_engine_metadata = MetaData()
db_engine = create_engine(
f"monetdb://{monetdb_username}:{monetdb_password}@" f"{monetdb_url}/{monetdb_farm}:"
diff --git a/mipengine/node/node_common_data_elements.py b/mipengine/node/node_common_data_elements.py
new file mode 100644
index 0000000000000000000000000000000000000000..01fc56c51082d0f92ff4eaaad1f9c869cbd3f329
--- /dev/null
+++ b/mipengine/node/node_common_data_elements.py
@@ -0,0 +1,4 @@
+from mipengine.common_data_elements import CommonDataElements
+from mipengine.node import config as node_config
+
+node_common_data_elements = CommonDataElements(node_config.cdes_metadata_path)
diff --git a/mipengine/resources/__init__.py b/mipengine/resources/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/mipengine/resources/pathologies_metadata/__init__.py b/mipengine/resources/pathologies_metadata/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/mipengine/resources/pathologies_metadata/dementia.json_original b/mipengine/resources/pathologies_metadata/dementia.json_original
deleted file mode 100755
index 1fcd04650cd85d7c06a26bfdbf880acdec01ce1b..0000000000000000000000000000000000000000
--- a/mipengine/resources/pathologies_metadata/dementia.json_original
+++ /dev/null
@@ -1,2434 +0,0 @@
-{
- "variables": [
- {
- "isCategorical": true,
- "code": "dataset",
- "sql_type": "text",
- "description": "Variable used to differentiate datasets",
- "enumerations": [
- {
- "code": "ppmi",
- "label": "PPMI"
- },
- {
- "code": "edsd",
- "label": "EDSD"
- },
- {
- "code": "desd-synthdata",
- "label": "DESD-synthdata"
- },
- {
- "code": "fake_longitudinal",
- "label": "Longitudinal"
- }
- ],
- "label": "Dataset",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "subjectvisitid",
- "sql_type": "text",
- "description": "The ID of the Patient’s Visit",
- "label": "Visit ID",
- "units": "",
- "type": "text",
- "methodology": ""
- },
- {
- "isCategorical": false,
- "code": "subjectvisitdate",
- "sql_type": "text",
- "description": "The date of the Patient’s Visit",
- "label": "Visit Date",
- "units": "",
- "type": "date",
- "methodology": ""
- }
- ],
- "code": "dementia",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "av45",
- "sql_type": "real",
- "description": "AV45 Average AV45 SUVR of frontal anterior cingulate precuneus and parietal cortex\\nrelative to the cerebellum",
- "label": "AV45",
- "units": "",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "fdg",
- "sql_type": "real",
- "description": "Average FDG-PET of angular temporal and posterior cingulate. Most important hypometabolic regions that are indicative of pathological metabolic change in MCI and AD.",
- "label": "FDG-PET",
- "units": "",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "pib",
- "sql_type": "real",
- "description": "Average PIB SUVR of frontal cortex anterior cingulate precuneus cortex and parietal cortex.",
- "label": "PIB",
- "units": "",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "pet",
- "label": "Pet"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "brainstem",
- "sql_type": "real",
- "description": "Brainstem volume",
- "label": "Brainstem",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "tiv",
- "sql_type": "real",
- "description": "Total intra-cranial volume",
- "label": "TIV",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "brain_anatomy",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "_3rdventricle",
- "sql_type": "real",
- "description": "",
- "label": "3rd Ventricle",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "_4thventricle",
- "sql_type": "real",
- "description": "",
- "label": "4th Ventricle",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "csfglobal",
- "sql_type": "real",
- "description": "",
- "label": "CSF global",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftinflatvent",
- "sql_type": "real",
- "description": "",
- "label": "Left inferior lateral ventricle",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftlateralventricle",
- "sql_type": "real",
- "description": "",
- "label": "Left lateral ventricle",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightinflatvent",
- "sql_type": "real",
- "description": "",
- "label": "Right inferior lateral ventricle",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightlateralventricle",
- "sql_type": "real",
- "description": "",
- "label": "Right lateral ventricle",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "csf_volume",
- "label": "Csf_volume"
- },
- {
- "code": "grey_matter_volume",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "cerebellarvermallobulesiv",
- "sql_type": "real",
- "description": "",
- "label": "Cerebellar Vermal Lobules I-V",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "cerebellarvermallobulesviiix",
- "sql_type": "real",
- "description": "",
- "label": "Cerebellar Vermal Lobules VIII-X",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "cerebellarvermallobulesvivii",
- "sql_type": "real",
- "description": "",
- "label": "Cerebellar Vermal Lobules VI-VII",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftcerebellumexterior",
- "sql_type": "real",
- "description": "",
- "label": "Left Cerebellum Exterior",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightcerebellumexterior",
- "sql_type": "real",
- "description": "",
- "label": "Right Cerebellum Exterior",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "cerebellum",
- "label": "Cerebellum"
- },
- {
- "code": "cerebral_nuclei",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftamygdala",
- "sql_type": "real",
- "description": "",
- "label": "Left Amygdala",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightamygdala",
- "sql_type": "real",
- "description": "",
- "label": "Right Amygdala",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "amygdala",
- "label": "Amygdala"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftaccumbensarea",
- "sql_type": "real",
- "description": "",
- "label": "Left Accumbens Area",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftbasalforebrain",
- "sql_type": "real",
- "description": "",
- "label": "Left Basal Forebrain",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftcaudate",
- "sql_type": "real",
- "description": "",
- "label": "Left Caudate",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftpallidum",
- "sql_type": "real",
- "description": "",
- "label": "Left Pallidum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftputamen",
- "sql_type": "real",
- "description": "",
- "label": "Left Putamen",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightaccumbensarea",
- "sql_type": "real",
- "description": "",
- "label": "Right Accumbens Area",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightbasalforebrain",
- "sql_type": "real",
- "description": "",
- "label": "Right Basal Forebrain",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightcaudate",
- "sql_type": "real",
- "description": "",
- "label": "Right Caudate",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightpallidum",
- "sql_type": "real",
- "description": "",
- "label": "Right Pallidum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightputamen",
- "sql_type": "real",
- "description": "",
- "label": "Right Putamen",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "basal_ganglia",
- "label": "Basal_ganglia"
- }
- ],
- "label": "Cerebral_nuclei"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftventraldc",
- "sql_type": "real",
- "description": "",
- "label": "Left Ventral DC",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightventraldc",
- "sql_type": "real",
- "description": "",
- "label": "Right Ventral DC",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "diencephalon",
- "label": "Diencephalon"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftaorganteriororbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left anterior orbital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftcocentraloperculum",
- "sql_type": "real",
- "description": "",
- "label": "Left central operculum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftfofrontaloperculum",
- "sql_type": "real",
- "description": "",
- "label": "Left frontal operculum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftfrpfrontalpole",
- "sql_type": "real",
- "description": "",
- "label": "Left frontal pole",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftgregyrusrectus",
- "sql_type": "real",
- "description": "",
- "label": "Left gyrus rectus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftlorglateralorbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left lateral orbital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmfcmedialfrontalcortex",
- "sql_type": "real",
- "description": "",
- "label": "Left medial frontal cortex",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmfgmiddlefrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left middle frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmorgmedialorbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left medial orbital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmprgprecentralgyrusmedialsegment",
- "sql_type": "real",
- "description": "",
- "label": "Left precentral gyrus medial segment",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmsfgsuperiorfrontalgyrusmedialsegment",
- "sql_type": "real",
- "description": "",
- "label": "Left superior frontal gyrus medial segment",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftopifgopercularpartoftheinferiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left opercular part of the inferior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftorifgorbitalpartoftheinferiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left orbital part of the inferior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftpoparietaloperculum",
- "sql_type": "real",
- "description": "",
- "label": "Left parietal operculum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftporgposteriororbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left posterior orbital gyrus",
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- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftprgprecentralgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left precentral gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftscasubcallosalarea",
- "sql_type": "real",
- "description": "",
- "label": "Left subcallosal area",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftsfgsuperiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left superior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftsmcsupplementarymotorcortex",
- "sql_type": "real",
- "description": "",
- "label": "Left supplementary motor cortex",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "lefttrifgtriangularpartoftheinferiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left triangular part of the inferior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightaorganteriororbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right anterior orbital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightcocentraloperculum",
- "sql_type": "real",
- "description": "",
- "label": "Right central operculum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightfofrontaloperculum",
- "sql_type": "real",
- "description": "",
- "label": "Right frontal operculum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightfrpfrontalpole",
- "sql_type": "real",
- "description": "",
- "label": "Right frontal pole",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightgregyrusrectus",
- "sql_type": "real",
- "description": "",
- "label": "Right gyrus rectus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightlorglateralorbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right lateral orbital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmfcmedialfrontalcortex",
- "sql_type": "real",
- "description": "",
- "label": "Right medial frontal cortex",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmfgmiddlefrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right middle frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmorgmedialorbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right medial orbital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmprgprecentralgyrusmedialsegment",
- "sql_type": "real",
- "description": "",
- "label": "Right precentral gyrus medial segment",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmsfgsuperiorfrontalgyrusmedialsegment",
- "sql_type": "real",
- "description": "",
- "label": "Right superior frontal gyrus medial segment",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightopifgopercularpartoftheinferiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right opercular part of the inferior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightorifgorbitalpartoftheinferiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right orbital part of the inferior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightpoparietaloperculum",
- "sql_type": "real",
- "description": "",
- "label": "Right parietal operculum",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightporgposteriororbitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right posterior orbital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightprgprecentralgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right precentral gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightscasubcallosalarea",
- "sql_type": "real",
- "description": "",
- "label": "Right subcallosal area",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightsfgsuperiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right superior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightsmcsupplementarymotorcortex",
- "sql_type": "real",
- "description": "",
- "label": "Right supplementary motor cortex",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "righttrifgtriangularpartoftheinferiorfrontalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right triangular part of the inferior frontal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "frontal",
- "label": "Frontal"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftainsanteriorinsula",
- "sql_type": "real",
- "description": "",
- "label": "Left anterior insula",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftpinsposteriorinsula",
- "sql_type": "real",
- "description": "",
- "label": "Left posterior insula",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightainsanteriorinsula",
- "sql_type": "real",
- "description": "",
- "label": "Right anterior insula",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightpinsposteriorinsula",
- "sql_type": "real",
- "description": "",
- "label": "Right posterior insula",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "insula",
- "label": "Insula"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftacgganteriorcingulategyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left anterior cingulate gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftententorhinalarea",
- "sql_type": "real",
- "description": "",
- "label": "Left entorhinal area",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "lefthippocampus",
- "sql_type": "real",
- "description": "",
- "label": "Left Hippocampus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmcggmiddlecingulategyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left middle cingulate gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftpcggposteriorcingulategyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left posterior cingulate gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftphgparahippocampalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left parahippocampal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftthalamusproper",
- "sql_type": "real",
- "description": "",
- "label": "Left Thalamus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightacgganteriorcingulategyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right anterior cingulate gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightententorhinalarea",
- "sql_type": "real",
- "description": "",
- "label": "Right entorhinal area",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "righthippocampus",
- "sql_type": "real",
- "description": "",
- "label": "Right Hippocampus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmcggmiddlecingulategyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right middle cingulate gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightpcggposteriorcingulategyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right posterior cingulate gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightphgparahippocampalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right parahippocampal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightthalamusproper",
- "sql_type": "real",
- "description": "",
- "label": "Right Thalamus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "limbic",
- "label": "Limbic"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftcalccalcarinecortex",
- "sql_type": "real",
- "description": "",
- "label": "Left calcarine cortex",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftcuncuneus",
- "sql_type": "real",
- "description": "",
- "label": "Left cuneus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftioginferioroccipitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left inferior occipital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftliglingualgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left lingual gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmogmiddleoccipitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left middle occipital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftocpoccipitalpole",
- "sql_type": "real",
- "description": "",
- "label": "Left occipital pole",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftofugoccipitalfusiformgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left occipital fusiform gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftsogsuperioroccipitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left superior occipital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightcalccalcarinecortex",
- "sql_type": "real",
- "description": "",
- "label": "Right calcarine cortex",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightcuncuneus",
- "sql_type": "real",
- "description": "",
- "label": "Right cuneus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightioginferioroccipitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right inferior occipital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightliglingualgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right lingual gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmogmiddleoccipitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right middle occipital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightocpoccipitalpole",
- "sql_type": "real",
- "description": "",
- "label": "Right occipital pole",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightofugoccipitalfusiformgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right occipital fusiform gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightsogsuperioroccipitalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right superior occipital gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "occipital",
- "label": "Occipital"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftangangulargyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left angular gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmpogpostcentralgyrusmedialsegment",
- "sql_type": "real",
- "description": "",
- "label": "Left postcentral gyrus medial segment",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftpcuprecuneus",
- "sql_type": "real",
- "description": "",
- "label": "Left precuneus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftpogpostcentralgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left postcentral gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftsmgsupramarginalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left supramarginal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftsplsuperiorparietallobule",
- "sql_type": "real",
- "description": "",
- "label": "Left superior parietal lobule",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightangangulargyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right angular gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmpogpostcentralgyrusmedialsegment",
- "sql_type": "real",
- "description": "",
- "label": "Right postcentral gyrus medial segment",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightpcuprecuneus",
- "sql_type": "real",
- "description": "",
- "label": "Right precuneus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightpogpostcentralgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right postcentral gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightsmgsupramarginalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right supramarginal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightsplsuperiorparietallobule",
- "sql_type": "real",
- "description": "",
- "label": "Right superior parietal lobule",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "parietal",
- "label": "Parietal"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftfugfusiformgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left fusiform gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftitginferiortemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left inferior temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftmtgmiddletemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left middle temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftppplanumpolare",
- "sql_type": "real",
- "description": "",
- "label": "Left planum polare",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftptplanumtemporale",
- "sql_type": "real",
- "description": "",
- "label": "Left planum temporale",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftstgsuperiortemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left superior temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "lefttmptemporalpole",
- "sql_type": "real",
- "description": "",
- "label": "Left temporal pole",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftttgtransversetemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Left transverse temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightfugfusiformgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right fusiform gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightitginferiortemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right inferior temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightmtgmiddletemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right middle temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightppplanumpolare",
- "sql_type": "real",
- "description": "",
- "label": "Right planum polare",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightptplanumtemporale",
- "sql_type": "real",
- "description": "",
- "label": "Right planum temporale",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightstgsuperiortemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right superior temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "righttmptemporalpole",
- "sql_type": "real",
- "description": "",
- "label": "Right temporal pole",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightttgtransversetemporalgyrus",
- "sql_type": "real",
- "description": "",
- "label": "Right transverse temporal gyrus",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "temporal",
- "label": "Temporal"
- }
- ],
- "label": "Grey_matter_volume"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "leftcerebellumwhitematter",
- "sql_type": "real",
- "description": "",
- "label": "Left Cerebellum White Matter",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "leftcerebralwhitematter",
- "sql_type": "real",
- "description": "",
- "label": "Left Cerebral White Matter",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "opticchiasm",
- "sql_type": "real",
- "description": "",
- "label": "Optic chiasm",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightcerebellumwhitematter",
- "sql_type": "real",
- "description": "",
- "label": "Right Cerebellum White Matter",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "rightcerebralwhitematter",
- "sql_type": "real",
- "description": "",
- "label": "Right Cerebral White Matter",
- "units": "cm3",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "white_matter_volume",
- "label": "White_matter_volume"
- }
- ],
- "label": "Brain_anatomy"
- },
- {
- "variables": [
- {
- "isCategorical": true,
- "code": "alzheimerbroadcategory",
- "sql_type": "text",
- "description": "There will be two broad categories taken into account. Alzheimer s disease (AD) in which the diagnostic is 100% certain and <Other> comprising the rest of Alzheimer s related categories. The <Other> category refers to Alzheime s related diagnosis which origin can be traced to other pathology eg. vascular. In this category MCI diagnosis can also be found. In summary all Alzheimer s related diagnosis that are not pure.",
- "enumerations": [
- {
- "code": "AD",
- "label": "Alzheimer’s disease"
- },
- {
- "code": "CN",
- "label": "Cognitively Normal"
- },
- {
- "code": "Other",
- "label": "Other"
- },
- {
- "code": "MCI",
- "label": "Mild cognitive impairment"
- }
- ],
- "label": "Alzheimer Broad Category",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "neurodegenerativescategories",
- "sql_type": "text",
- "description": "There will be two broad categories taken into account. Parkinson s disease without disability or light disability: Without fluctuation of the effect. Dementia in Parkinson s disease",
- "enumerations": [
- {
- "code": "PD",
- "label": "Parkinson’s disease"
- },
- {
- "code": "AD",
- "label": "Alzheimer’s disease"
- },
- {
- "code": "HD",
- "label": "Huntington’s disease\""
- },
- {
- "code": "ALS",
- "label": "Amyotrophic lateral sclerosis"
- },
- {
- "code": "BD",
- "label": "Batten disease"
- },
- {
- "code": "MCI",
- "label": "MCI"
- },
- {
- "code": "LBD",
- "label": "Lewy body dementia"
- },
- {
- "code": "CJD",
- "label": "Creutzfeldt Jakob disease"
- },
- {
- "code": "FTD",
- "label": "Frontotemporal dementia"
- },
- {
- "code": "MS",
- "label": "Multiple sclerosis"
- },
- {
- "code": "CN",
- "label": "Cognitively normal"
- }
- ],
- "label": "Neurodegeneratives categories",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "parkinsonbroadcategory",
- "sql_type": "text",
- "description": "There will be two broad categories taken into account. Parkinson s disease without disability or light disability: Without fluctuation of the effect. Dementia in Parkinson s disease",
- "enumerations": [
- {
- "code": "PD",
- "label": "Dementia in Parkinson''s disease"
- },
- {
- "code": "CN",
- "label": "Healthy control"
- },
- {
- "code": "Other",
- "label": "Parkinson''s disease without disability or light disability: Without fluctuation of the effect"
- }
- ],
- "label": "Parkinson Broad Category",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- }
- ],
- "code": "diagnosis",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": true,
- "code": "adnicategory",
- "sql_type": "text",
- "description": "Terms aggregating illnesses into classes. Note that the diagnosis in this categories are given only for the ADNI data set.",
- "enumerations": [
- {
- "code": "AD",
- "label": "Alzheimer’s Disease"
- },
- {
- "code": "MCI",
- "label": "Mild Cognitive Impairment"
- },
- {
- "code": "CN",
- "label": "Cognitively Normal"
- }
- ],
- "label": "ADNI category",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "edsdcategory",
- "sql_type": "text",
- "description": "Terms aggregating illnesses into classes. Note that the diagnosis in this categories are given only for the EDSD data set.",
- "enumerations": [
- {
- "code": "AD",
- "label": "Alzheimer’s Disease"
- },
- {
- "code": "MCI",
- "label": "Mild Cognitive Impairment"
- },
- {
- "code": "CN",
- "label": "Cognitively Normal"
- }
- ],
- "label": "EDSD category",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "ppmicategory",
- "sql_type": "text",
- "description": "Terms aggregating the Parkinson s diseases into classes. For this instance the diagnosis given at enrollment is taken as the clinical diagnosis. Note that the diagnosis in this categories are given only for the PPMI data set.",
- "enumerations": [
- {
- "code": "PD",
- "label": "Parkinson disease"
- },
- {
- "code": "HC",
- "label": "Healthy controls"
- },
- {
- "code": "PRODROMA",
- "label": "Prodromal"
- },
- {
- "code": "GENPD",
- "label": "Genetic PD patients with a mutation (LRRK2, GBA or SNCA)"
- },
- {
- "code": "REGUN",
- "label": "Genetic Unaffected patients with a mutation (LRRK2, GBA or SNCA)"
- },
- {
- "code": "REGPD",
- "label": "Genetic registry PD subjects with a mutation (LRRK2, GBA or SNCA)"
- }
- ],
- "label": "PPMI category",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- }
- ],
- "code": "dataset_specific_diagnosis",
- "label": "Dataset_specific_diagnosis"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "DIAG_etiology_1",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:etiology:1",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_etiology_2",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:etiology:2",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_etiology_3",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:etiology:3",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_lng",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:lng",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_lngapp",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:lngapp",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_stade",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:stade",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_stademin",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:stademin",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_syndamn",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:syndamn",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_syndoth",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:syndoth",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "DIAG_syndr",
- "sql_type": "text",
- "description": "",
- "label": "DIAG:syndr",
- "units": "",
- "type": "text",
- "methodology": "mip-cde"
- }
- ],
- "code": "bna",
- "label": "Bna"
- }
- ],
- "label": "Diagnosis"
- },
- {
- "variables": [
- {
- "isCategorical": false,
- "minValue": 0,
- "code": "minimentalstate",
- "maxValue": 30,
- "sql_type": "int",
- "description": "The Mini Mental State Examination (MMSE) or Folstein test is a 30-point questionnaire that is used extensively in clinical and research settings to measure cognitive impairment. It is commonly used to screen for dementia.",
- "label": "MMSE Total scores",
- "units": "",
- "type": "integer",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "minValue": 0,
- "code": "montrealcognitiveassessment",
- "maxValue": 30,
- "sql_type": "int",
- "description": "The Montreal Cognitive Assessment (MoCA) was designed as a rapid screening instrument for mild cognitive dysfunction. It assesses different cognitive domains: attention and concentration executive functions memory language visuoconstructional skills conceptual thinking calculations and orientation. MoCA Total Scores refer to the final count obtained by patients after the complete test is performed.",
- "label": "MoCA Total",
- "units": "",
- "type": "integer",
- "methodology": "mip-cde"
- }
- ],
- "code": "neuropsychology",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": true,
- "code": "updrshy",
- "sql_type": "text",
- "description": "The Hoehn and Yahr scale (HY) is a widely used clinical rating scale which defines broad categories of motor function in Parkinson\\u2019s disease (PD). It captures typical patterns of progressive motor impairment.",
- "enumerations": [
- {
- "code": "1",
- "label": "Unilateral involvement only usually with minimal or no functional disability"
- },
- {
- "code": "2",
- "label": "Bilateral or midline involvement without impairment of balance"
- },
- {
- "code": "3",
- "label": "Bilateral disease: mild to moderate disability with impaired postural reflexes; physically independent"
- },
- {
- "code": "4",
- "label": "Severely disabling disease; still able to walk or stand unassisted"
- },
- {
- "code": "5",
- "label": "Confinement to bed or wheelchair unless aided"
- }
- ],
- "label": "UPDRS HY",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "minValue": 0,
- "code": "updrstotal",
- "maxValue": 172,
- "sql_type": "int",
- "description": "The unified Parkinson s disease rating scale (UPDRS) is used to follow the longitudinal course of Parkinson s disease. The UPD rating scale is the most commonly used scale in the clinical study of Parkinson s disease.",
- "label": "UPDRS Total",
- "units": "",
- "type": "integer",
- "methodology": "mip-cde"
- }
- ],
- "code": "updrs",
- "label": "Updrs"
- }
- ],
- "label": "Neuropsychology"
- },
- {
- "variables": [
- {
- "isCategorical": true,
- "code": "agegroup",
- "sql_type": "text",
- "description": "Age Group",
- "enumerations": [
- {
- "code": "-50y",
- "label": "-50y"
- },
- {
- "code": "50-59y",
- "label": "50-59y"
- },
- {
- "code": "60-69y",
- "label": "60-69y"
- },
- {
- "code": "70-79y",
- "label": "70-79y"
- },
- {
- "code": "+80y",
- "label": "+80y"
- }
- ],
- "label": "agegroup",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "gender",
- "sql_type": "text",
- "description": "Gender of the patient - Sex assigned at birth",
- "enumerations": [
- {
- "code": "M",
- "label": "Male"
- },
- {
- "code": "F",
- "label": "Female"
- }
- ],
- "label": "Gender",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "handedness",
- "sql_type": "text",
- "description": "Describes the tendency of the patient to use either the right or the left hand more naturally than the other.",
- "enumerations": [
- {
- "code": "R",
- "label": "Right"
- },
- {
- "code": "L",
- "label": "Left"
- },
- {
- "code": "A",
- "label": "Ambidextrous"
- }
- ],
- "label": "Handedness",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "minValue": 0,
- "code": "subjectage",
- "maxValue": 130,
- "sql_type": "real",
- "description": "Exact age of the subject for datasets that allow such precision.",
- "label": "Exact age",
- "units": "years",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "minValue": 0,
- "code": "subjectageyears",
- "maxValue": 130,
- "sql_type": "int",
- "description": "Subject age in years.",
- "label": "Age Years",
- "units": "years",
- "type": "integer",
- "methodology": "mip-cde"
- }
- ],
- "code": "demographics",
- "label": "Demographics"
- },
- {
- "code": "genetic",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": true,
- "code": "apoe4",
- "sql_type": "text",
- "description": "Apolipoprotein E (APOE) e4 allele: is the strongest risk factor for Late Onset Alzheimer Disease (LOAD). At least one copy of APOE-e4 ",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "ApoE4",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs10498633_t",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs10498633_T",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs11136000_t",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs11136000_T",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs11767557_c",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs11767557_C",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs1476679_c",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs1476679_C",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs17125944_c",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs17125944_C",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs190982_g",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs190982_G",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs2718058_g",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs2718058_G",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs3764650_g",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs3764650_G",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs3818361_t",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs3818361_T",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs3851179_a",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs3851179_A",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs3865444_t",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs3865444_T",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs610932_a",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs610932_A",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": true,
- "code": "rs744373_c",
- "sql_type": "text",
- "description": "",
- "enumerations": [
- {
- "code": "0",
- "label": "0"
- },
- {
- "code": "1",
- "label": "1"
- },
- {
- "code": "2",
- "label": "2"
- }
- ],
- "label": "rs744373_C",
- "units": "",
- "type": "nominal",
- "methodology": "mip-cde"
- }
- ],
- "code": "polymorphism",
- "label": "Polymorphism"
- }
- ],
- "label": "Genetic"
- },
- {
- "code": "proteome",
- "groups": [
- {
- "variables": [
- {
- "isCategorical": false,
- "code": "ab1_42",
- "sql_type": "real",
- "description": "A\\u03b2 is the main component of amyloid plaques (extracellular deposits found in the brains of patients with Alzheimer’s disease). Similar plaques appear in some variants of Lewy body dementia and in inclusion body myositis (a muscle disease), while A\\u03b2 can also form the aggregates that coat cerebral blood vessels in cerebral amyloid angiopathy. The plaques are composed of a tangle of regularly ordered fibrillar aggregates called amyloid fibers, a protein fold shared by other peptides such as the prions associated with protein misfolding diseases.",
- "label": "Level of amyloid beta 1-42 peptides in cerebrospinal fluid",
- "units": "",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "ab1_40",
- "sql_type": "real",
- "description": "A\\u03b2 is the main component of amyloid plaques (extracellular deposits found in the brains of patients with Alzheimer's disease). Similar plaques appear in some variants of Lewy body dementia and in inclusion body myositis (a muscle disease), while A\\u03b2 can also form the aggregates that coat cerebral blood vessels in cerebral amyloid angiopathy. The plaques are composed of a tangle of regularly ordered fibrillar aggregates called amyloid fibers, a protein fold shared by other peptides such as the prions associated with protein misfolding diseases.",
- "label": "Level od amyloid beta 1-40 peptides ion cerebrospinal fluid",
- "units": "",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "t_tau",
- "sql_type": "real",
- "description": "Tau proteins (or \\u03c4 proteins) are proteins that stabilize microtubules. They are abundant in neurons of the central nervous system and are less common elsewhere, but are also expressed at very low levels in CNS astrocytes and oligodendrocytes. Pathologies and dementias of the nervous system such as Alzheimer’s disease and Parkinson’s disease are associated with tau proteins that have become defective and no longer stabilize microtubules properly.",
- "label": "Total level of tau proteins in cerebrospinal fluid",
- "units": "",
- "type": "real",
- "methodology": "mip-cde"
- },
- {
- "isCategorical": false,
- "code": "p_tau",
- "sql_type": "real",
- "description": "Hyperphosphorylation of the tau protein (tau inclusions, pTau) can result in the self-assembly of tangles of paired helical filaments and straight filaments, which are involved in the pathogenesis of Alzheimer's disease, frontotemporal dementia, and other tauopathies.",
- "label": "Level of phosphorylated tau proteins in cerebrospinal fluid",
- "units": "",
- "type": "real",
- "methodology": "mip-cde"
- }
- ],
- "code": "csf_proteome",
- "label": "Csf_proteome"
- }
- ],
- "label": "Proteome"
- }
- ],
- "label": "Dementia"
-}
diff --git a/tasks.py b/tasks.py
index 9b5ae0f853d86522bbec6fc134e74c480ed6cbf8..46f7b689a8fa52fd7c1c30b16dcacbf07caee85c 100644
--- a/tasks.py
+++ b/tasks.py
@@ -104,6 +104,8 @@ def create_node_configs(c):
for node in deployment_config["nodes"]:
node_config = template_node_config.copy()
+ node_config["cdes_metadata_path"] = deployment_config["cdes_metadata_path"]
+
node_config["node_registry"]["ip"] = deployment_config["ip"]
node_config["node_registry"]["port"] = deployment_config["node_registry_port"]
@@ -127,7 +129,7 @@ def create_node_configs(c):
template_controller_config = toml.load(fp)
controller_config = template_controller_config.copy()
-
+ controller_config["cdes_metadata_path"] = deployment_config["cdes_metadata_path"]
controller_config["node_registry"]["ip"] = deployment_config["ip"]
controller_config["node_registry"]["port"] = deployment_config["node_registry_port"]
diff --git a/mipengine/resources/pathologies_metadata/dementia.json b/tests/demo_data/dementia/CDEsMetadata.json
similarity index 100%
rename from mipengine/resources/pathologies_metadata/dementia.json
rename to tests/demo_data/dementia/CDEsMetadata.json
diff --git a/mipengine/resources/pathologies_metadata/mentalhealth.json b/tests/demo_data/mentalhealth/CDEsMetadata.json
similarity index 100%
rename from mipengine/resources/pathologies_metadata/mentalhealth.json
rename to tests/demo_data/mentalhealth/CDEsMetadata.json
diff --git a/mipengine/resources/pathologies_metadata/tbi.json b/tests/demo_data/tbi/CDEsMetadata.json
similarity index 100%
rename from mipengine/resources/pathologies_metadata/tbi.json
rename to tests/demo_data/tbi/CDEsMetadata.json
diff --git a/tests/e2e_tests/deployment_template.toml b/tests/e2e_tests/deployment_template.toml
index cc25f8ab87c34f53b5bc222bfc8f57cd3e25b903..f4172dae9023f1fbaeeff3f75ec9ce193e83e9d8 100644
--- a/tests/e2e_tests/deployment_template.toml
+++ b/tests/e2e_tests/deployment_template.toml
@@ -4,6 +4,8 @@ celery_log_level ="INFO"
monetdb_image = "madgik/mipenginedb:latest"
rabbitmq_image = "madgik/mipengine_rabbitmq:latest"
+cdes_metadata_path = "./tests/demo_data"
+
node_registry_port = 8500
diff --git a/tests/integration_tests/deployment_template.toml b/tests/integration_tests/deployment_template.toml
index cc25f8ab87c34f53b5bc222bfc8f57cd3e25b903..f4172dae9023f1fbaeeff3f75ec9ce193e83e9d8 100644
--- a/tests/integration_tests/deployment_template.toml
+++ b/tests/integration_tests/deployment_template.toml
@@ -4,6 +4,8 @@ celery_log_level ="INFO"
monetdb_image = "madgik/mipenginedb:latest"
rabbitmq_image = "madgik/mipengine_rabbitmq:latest"
+cdes_metadata_path = "./tests/demo_data"
+
node_registry_port = 8500
diff --git a/tests/unit_tests/test_filters.py b/tests/unit_tests/test_filters.py
index 90b52f8168e57b0b17fc738c9420bc16f42f198c..97bfb29af0824bd865dc31a738829131e19b73b2 100644
--- a/tests/unit_tests/test_filters.py
+++ b/tests/unit_tests/test_filters.py
@@ -1,8 +1,130 @@
+from unittest.mock import patch
+
import pytest
+from mipengine.common_data_elements import CommonDataElement
+from mipengine.common_data_elements import CommonDataElements
+from mipengine.common_data_elements import MetadataEnumeration
+from mipengine.common_data_elements import MetadataVariable
from mipengine.filters import build_filter_clause, validate_proper_filter
-PATHOLOGY = "tbi"
+PATHOLOGY = "test_pathology1"
+
+
+@pytest.fixture()
+def common_data_elements():
+ common_data_elements = CommonDataElements()
+ common_data_elements.pathologies = {
+ "test_pathology1": {
+ "test_age_value": CommonDataElement(
+ MetadataVariable(
+ code="test_age_value",
+ label="test test_age_value",
+ sql_type="int",
+ isCategorical=False,
+ enumerations=None,
+ min=0,
+ max=130,
+ )
+ ),
+ "test_pupil_reactivity_right_eye_result": CommonDataElement(
+ MetadataVariable(
+ code="test_pupil_reactivity_right_eye_result",
+ label="test test_pupil_reactivity_right_eye_result",
+ sql_type="text",
+ isCategorical=True,
+ enumerations=[
+ MetadataEnumeration(code="Sluggish", label="Sluggish"),
+ MetadataEnumeration(code="Nonreactive", label="Nonreactive"),
+ MetadataEnumeration(code="Brisk", label="Brisk"),
+ MetadataEnumeration(code="Untestable", label="Untestable"),
+ MetadataEnumeration(code="Unknown", label="Unknown"),
+ ],
+ min=None,
+ max=None,
+ )
+ ),
+ "test_mortality_core": CommonDataElement(
+ MetadataVariable(
+ code="test_mortality_core",
+ label="test_mortality_core",
+ sql_type="real",
+ isCategorical=False,
+ enumerations=None,
+ min=None,
+ max=None,
+ )
+ ),
+ "test_gose_score": CommonDataElement(
+ MetadataVariable(
+ code="test_gose_score",
+ label="test_gose_score",
+ sql_type="text",
+ isCategorical=True,
+ enumerations=[
+ MetadataEnumeration(code="1", label="Dead"),
+ MetadataEnumeration(code="2", label="Vegetative State"),
+ MetadataEnumeration(code="3", label="Lower Severe Disability"),
+ MetadataEnumeration(code="4", label="Upper Severe Disability"),
+ MetadataEnumeration(
+ code="5", label="Lower Moderate Disability"
+ ),
+ MetadataEnumeration(
+ code="6", label="Upper Moderate Disability"
+ ),
+ MetadataEnumeration(code="7", label="Lower Good Recovery"),
+ MetadataEnumeration(code="8", label="Upper Good Recovery"),
+ ],
+ min=None,
+ max=None,
+ )
+ ),
+ "test_gcs_total_score": CommonDataElement(
+ MetadataVariable(
+ code="test_gcs_total_score",
+ label="test_gcs_total_score",
+ sql_type="text",
+ isCategorical=True,
+ enumerations=[
+ MetadataEnumeration(code="3", label="3"),
+ MetadataEnumeration(code="4", label="4"),
+ MetadataEnumeration(code="5", label="5"),
+ MetadataEnumeration(code="6", label="6"),
+ MetadataEnumeration(code="7", label="7"),
+ MetadataEnumeration(code="8", label="8"),
+ MetadataEnumeration(code="9", label="9"),
+ MetadataEnumeration(code="10", label="10"),
+ MetadataEnumeration(code="11", label="11"),
+ MetadataEnumeration(code="12", label="12"),
+ MetadataEnumeration(code="13", label="13"),
+ MetadataEnumeration(code="14", label="14"),
+ MetadataEnumeration(code="15", label="15"),
+ MetadataEnumeration(code="untestable", label="untestable"),
+ MetadataEnumeration(code="unknown", label="unknown"),
+ ],
+ min=None,
+ max=None,
+ )
+ ),
+ "test_gender_type": CommonDataElement(
+ MetadataVariable(
+ code="test_gender_type",
+ label="test_gender_type",
+ sql_type="text",
+ isCategorical=True,
+ enumerations=[
+ MetadataEnumeration(code="M", label="Male"),
+ MetadataEnumeration(code="F", label="Female"),
+ ],
+ min=None,
+ max=None,
+ )
+ ),
+ },
+ }
+
+ return common_data_elements
+
all_success_cases = [
(
@@ -10,8 +132,8 @@ all_success_cases = [
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
@@ -20,15 +142,15 @@ all_success_cases = [
],
"valid": True,
},
- "age_value = 17",
+ "test_age_value = 17",
),
(
{
"condition": "AND",
"rules": [
{
- "id": "pupil_reactivity_right_eye_result",
- "field": "pupil_reactivity_right_eye_result",
+ "id": "test_pupil_reactivity_right_eye_result",
+ "field": "test_pupil_reactivity_right_eye_result",
"type": "string",
"input": "text",
"operator": "not_equal",
@@ -37,23 +159,23 @@ all_success_cases = [
],
"valid": True,
},
- "pupil_reactivity_right_eye_result <> 'Nonreactive'",
+ "test_pupil_reactivity_right_eye_result <> 'Nonreactive'",
),
(
{
"condition": "OR",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
"value": 17,
},
{
- "id": "pupil_reactivity_right_eye_result",
- "field": "pupil_reactivity_right_eye_result",
+ "id": "test_pupil_reactivity_right_eye_result",
+ "field": "test_pupil_reactivity_right_eye_result",
"type": "string",
"input": "text",
"operator": "not_equal",
@@ -62,23 +184,23 @@ all_success_cases = [
],
"valid": True,
},
- "age_value = 17 OR pupil_reactivity_right_eye_result <> 'Nonreactive'",
+ "test_age_value = 17 OR test_pupil_reactivity_right_eye_result <> 'Nonreactive'",
),
(
{
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "less",
"value": 50,
},
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "greater",
@@ -87,23 +209,23 @@ all_success_cases = [
],
"valid": True,
},
- "age_value < 50 AND age_value > 20",
+ "test_age_value < 50 AND test_age_value > 20",
),
(
{
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "not_between",
"value": [60, 90],
},
{
- "id": "mortality_core",
- "field": "mortality_core",
+ "id": "test_mortality_core",
+ "field": "test_mortality_core",
"type": "double",
"input": "number",
"operator": "between",
@@ -112,23 +234,23 @@ all_success_cases = [
],
"valid": True,
},
- "NOT age_value BETWEEN 60 AND 90 AND mortality_core BETWEEN 0.3 AND 0.8",
+ "NOT test_age_value BETWEEN 60 AND 90 AND test_mortality_core BETWEEN 0.3 AND 0.8",
),
(
{
"condition": "OR",
"rules": [
{
- "id": "gose_score",
- "field": "gose_score",
+ "id": "test_gose_score",
+ "field": "test_gose_score",
"type": "text",
"input": "text",
"operator": "is_null",
"value": None,
},
{
- "id": "gcs_total_score",
- "field": "gcs_total_score",
+ "id": "test_gcs_total_score",
+ "field": "test_gcs_total_score",
"type": "int",
"input": "number",
"operator": "is_not_null",
@@ -137,15 +259,15 @@ all_success_cases = [
],
"valid": True,
},
- "gose_score IS NULL OR gcs_total_score IS NOT NULL",
+ "test_gose_score IS NULL OR test_gcs_total_score IS NOT NULL",
),
(
{
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "integer",
"input": "number",
"operator": "in",
@@ -154,15 +276,15 @@ all_success_cases = [
],
"valid": True,
},
- "age_value IN (17,19)",
+ "test_age_value IN (17,19)",
),
(
{
"condition": "AND",
"rules": [
{
- "id": "gender_type",
- "field": "gender_type",
+ "id": "test_gender_type",
+ "field": "test_gender_type",
"type": "string",
"input": "text",
"operator": "in",
@@ -171,7 +293,7 @@ all_success_cases = [
],
"valid": True,
},
- "gender_type IN ('F','M')",
+ "test_gender_type IN ('F','M')",
),
(
{
@@ -181,8 +303,8 @@ all_success_cases = [
"condition": "AND",
"rules": [
{
- "id": "gender_type",
- "field": "gender_type",
+ "id": "test_gender_type",
+ "field": "test_gender_type",
"type": "string",
"input": "text",
"operator": "equal",
@@ -192,16 +314,16 @@ all_success_cases = [
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "between",
"value": [20, 30],
},
{
- "id": "gose_score",
- "field": "gose_score",
+ "id": "test_gose_score",
+ "field": "test_gose_score",
"type": "text",
"input": "text",
"operator": "is_not_null",
@@ -215,8 +337,8 @@ all_success_cases = [
"condition": "AND",
"rules": [
{
- "id": "gender_type",
- "field": "gender_type",
+ "id": "test_gender_type",
+ "field": "test_gender_type",
"type": "string",
"input": "text",
"operator": "not_equal",
@@ -226,16 +348,16 @@ all_success_cases = [
"condition": "AND",
"rules": [
{
- "id": "mortality_core",
- "field": "mortality_core",
+ "id": "test_mortality_core",
+ "field": "test_mortality_core",
"type": "double",
"input": "number",
"operator": "greater",
"value": 0.5,
},
{
- "id": "mortality_core",
- "field": "mortality_core",
+ "id": "test_mortality_core",
+ "field": "test_mortality_core",
"type": "double",
"input": "number",
"operator": "less_or_equal",
@@ -249,8 +371,8 @@ all_success_cases = [
"valid": True,
},
(
- "gender_type = 'F' AND age_value BETWEEN 20 AND 30 AND gose_score IS NOT NULL OR gender_type <> 'F' AND "
- "mortality_core > 0.5 AND mortality_core <= 0.8"
+ "test_gender_type = 'F' AND test_age_value BETWEEN 20 AND 30 AND test_gose_score IS NOT NULL OR test_gender_type <> 'F' AND "
+ "test_mortality_core > 0.5 AND test_mortality_core <= 0.8"
),
),
]
@@ -262,8 +384,8 @@ def test_build_filter_clause(test_input, expected):
@pytest.mark.parametrize("test_input,expected", all_success_cases)
-def test_validate_proper_filter(test_input, expected):
- validate_proper_filter(PATHOLOGY, test_input)
+def test_validate_proper_filter(test_input, expected, common_data_elements):
+ validate_proper_filter(common_data_elements, PATHOLOGY, test_input)
all_build_filter_clause_fail_cases = [
@@ -272,8 +394,8 @@ all_build_filter_clause_fail_cases = [
"condition": "ANDOR",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
@@ -296,8 +418,8 @@ all_validate_proper_filter_fail_cases = [
"condition": "ANDOR",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
@@ -317,8 +439,8 @@ all_validate_proper_filter_fail_cases = [
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "invalid operator",
@@ -335,7 +457,7 @@ all_validate_proper_filter_fail_cases = [
"rules": [
{
"id": "invalid column",
- "field": "age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
@@ -351,8 +473,8 @@ all_validate_proper_filter_fail_cases = [
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
@@ -368,8 +490,8 @@ all_validate_proper_filter_fail_cases = [
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
@@ -386,9 +508,11 @@ all_validate_proper_filter_fail_cases = [
@pytest.mark.parametrize(
"test_input,expected_error", all_validate_proper_filter_fail_cases
)
-def test_validate_proper_filter_fail_cases(test_input, expected_error):
+def test_validate_proper_filter_fail_cases(
+ test_input, expected_error, common_data_elements
+):
with pytest.raises(expected_error):
- validate_proper_filter(PATHOLOGY, test_input)
+ validate_proper_filter(common_data_elements, PATHOLOGY, test_input)
@pytest.mark.parametrize(
@@ -403,16 +527,17 @@ invalid_pathology_case = ["non_existing_pathology", 0, True]
@pytest.mark.parametrize("pathology", invalid_pathology_case)
-def test_validate_proper_filter_fail_cases(pathology):
+def test_validate_proper_filter_fail_cases(pathology, common_data_elements):
with pytest.raises(KeyError):
validate_proper_filter(
+ common_data_elements,
pathology,
{
"condition": "AND",
"rules": [
{
- "id": "age_value",
- "field": "age_value",
+ "id": "test_age_value",
+ "field": "test_age_value",
"type": "int",
"input": "number",
"operator": "equal",
diff --git a/tests/unit_tests/test_validate_algorithm_request.py b/tests/unit_tests/test_validate_algorithm_request.py
index 22f7baf5a29aae41e68b0e78508c3e820932aeeb..d27945fd52ef9e7d73ec8bba1e027a615c58941a 100644
--- a/tests/unit_tests/test_validate_algorithm_request.py
+++ b/tests/unit_tests/test_validate_algorithm_request.py
@@ -140,7 +140,7 @@ def mock_cdes():
}
with patch(
- "mipengine.controller.api.validator.common_data_elements",
+ "mipengine.controller.api.validator.controller_common_data_elements",
common_data_elements,
):
yield