[ENH] Add API response examples and code to generate them

api-responses/fapi_query_fail_207.json

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+{
+  "errors": [
+    {
+      "node_name": "2 OpenNeuro Datasets",
+      "error": "Request failed due to a network error or because the node API could not be reached: [Errno -3] Temporary failure in name resolution"
+    },
+    {
+      "node_name": "BIDS Synthetic",
+      "error": "Request failed due to a network error or because the node API could not be reached: [Errno -2] Name or service not known"
+    }
+  ],
+  "responses": [],
+  "nodes_response_status": "fail"
+}

api-responses/fapi_query_partial_success_207.json

@@ -0,0 +1,41 @@
+{
+  "errors": [
+    {
+      "node_name": "BIDS Synthetic",
+      "error": "Request failed due to a network error or because the node API could not be reached: [Errno -2] Name or service not known"
+    }
+  ],
+  "responses": [
+    {
+      "node_name": "2 OpenNeuro Datasets",
+      "dataset_uuid": "http://neurobagel.org/vocab/1c9a29d8-9ce7-4bb6-9c44-f33ac504bcb4",
+      "dataset_name": "Balloon Analog Risk-taking Task",
+      "dataset_portal_uri": "https://github.com/OpenNeuroDatasets-JSONLD/ds000001.git",
+      "dataset_total_subjects": 16,
+      "records_protected": true,
+      "num_matching_subjects": 10,
+      "subject_data": "protected",
+      "image_modals": [
+        "http://purl.org/nidash/nidm#T2Weighted",
+        "http://purl.org/nidash/nidm#T1Weighted",
+        "http://purl.org/nidash/nidm#FlowWeighted"
+      ]
+    },
+    {
+      "node_name": "2 OpenNeuro Datasets",
+      "dataset_uuid": "http://neurobagel.org/vocab/c7bb6a5b-4066-4a59-b56c-3c6fe4d44b90",
+      "dataset_name": "Classification learning",
+      "dataset_portal_uri": "https://github.com/OpenNeuroDatasets-JSONLD/ds000002.git",
+      "dataset_total_subjects": 17,
+      "records_protected": true,
+      "num_matching_subjects": 10,
+      "subject_data": "protected",
+      "image_modals": [
+        "http://purl.org/nidash/nidm#T2Weighted",
+        "http://purl.org/nidash/nidm#T1Weighted",
+        "http://purl.org/nidash/nidm#FlowWeighted"
+      ]
+    }
+  ],
+  "nodes_response_status": "partial success"
+}

api-responses/fapi_query_success_200.json

@@ -0,0 +1,218 @@
+{
+  "errors": [],
+  "responses": [
+    {
+      "node_name": "2 OpenNeuro Datasets",
+      "dataset_uuid": "http://neurobagel.org/vocab/1c9a29d8-9ce7-4bb6-9c44-f33ac504bcb4",
+      "dataset_name": "Balloon Analog Risk-taking Task",
+      "dataset_portal_uri": "https://github.com/OpenNeuroDatasets-JSONLD/ds000001.git",
+      "dataset_total_subjects": 16,
+      "records_protected": true,
+      "num_matching_subjects": 10,
+      "subject_data": "protected",
+      "image_modals": [
+        "http://purl.org/nidash/nidm#T2Weighted",
+        "http://purl.org/nidash/nidm#T1Weighted",
+        "http://purl.org/nidash/nidm#FlowWeighted"
+      ]
+    },
+    {
+      "node_name": "2 OpenNeuro Datasets",
+      "dataset_uuid": "http://neurobagel.org/vocab/c7bb6a5b-4066-4a59-b56c-3c6fe4d44b90",
+      "dataset_name": "Classification learning",
+      "dataset_portal_uri": "https://github.com/OpenNeuroDatasets-JSONLD/ds000002.git",
+      "dataset_total_subjects": 17,
+      "records_protected": true,
+      "num_matching_subjects": 10,
+      "subject_data": "protected",
+      "image_modals": [
+        "http://purl.org/nidash/nidm#T2Weighted",
+        "http://purl.org/nidash/nidm#T1Weighted",
+        "http://purl.org/nidash/nidm#FlowWeighted"
+      ]
+    },
+    {
+      "node_name": "BIDS Synthetic",
+      "dataset_uuid": "http://neurobagel.org/vocab/e0c7d08c-edcc-4c2a-816a-306878ed7be2",
+      "dataset_name": "BIDS synthetic",
+      "dataset_portal_uri": "https://github.com/bids-standard/bids-examples",
+      "dataset_total_subjects": 5,
+      "records_protected": false,
+      "num_matching_subjects": 2,
+      "subject_data": [
+        {
+          "sub_id": "sub-01",
+          "session_id": "ses-01",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/ImagingSession",
+          "age": null,
+          "sex": null,
+          "diagnosis": [
+            null
+          ],
+          "subject_group": null,
+          "assessment": [
+            null
+          ],
+          "image_modal": [
+            "http://purl.org/nidash/nidm#T1Weighted",
+            "http://purl.org/nidash/nidm#FlowWeighted"
+          ],
+          "session_file_path": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01"
+        },
+        {
+          "sub_id": "sub-01",
+          "session_id": "ses-01",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/PhenotypicSession",
+          "age": 34.1,
+          "sex": "http://purl.bioontology.org/ontology/SNOMEDCT/248152002",
+          "diagnosis": [
+            null
+          ],
+          "subject_group": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C94342",
+          "assessment": [
+            "https://www.cognitiveatlas.org/task/id/trm_57964b8a66aed",
+            "https://www.cognitiveatlas.org/task/id/tsk_4a57abb949ece"
+          ],
+          "image_modal": [
+            null
+          ],
+          "session_file_path": null
+        },
+        {
+          "sub_id": "sub-01",
+          "session_id": "ses-02",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/ImagingSession",
+          "age": null,
+          "sex": null,
+          "diagnosis": [
+            null
+          ],
+          "subject_group": null,
+          "assessment": [
+            null
+          ],
+          "image_modal": [
+            "http://purl.org/nidash/nidm#T1Weighted",
+            "http://purl.org/nidash/nidm#FlowWeighted"
+          ],
+          "session_file_path": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-02"
+        },
+        {
+          "sub_id": "sub-01",
+          "session_id": "ses-02",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/PhenotypicSession",
+          "age": 35.3,
+          "sex": "http://purl.bioontology.org/ontology/SNOMEDCT/248152002",
+          "diagnosis": [
+            null
+          ],
+          "subject_group": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C94342",
+          "assessment": [
+            "https://www.cognitiveatlas.org/task/id/trm_57964b8a66aed",
+            "https://www.cognitiveatlas.org/task/id/tsk_4a57abb949ece"
+          ],
+          "image_modal": [
+            null
+          ],
+          "session_file_path": null
+        },
+        {
+          "sub_id": "sub-04",
+          "session_id": "ses-01",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/ImagingSession",
+          "age": null,
+          "sex": null,
+          "diagnosis": [
+            null
+          ],
+          "subject_group": null,
+          "assessment": [
+            null
+          ],
+          "image_modal": [
+            "http://purl.org/nidash/nidm#T1Weighted",
+            "http://purl.org/nidash/nidm#FlowWeighted"
+          ],
+          "session_file_path": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-01"
+        },
+        {
+          "sub_id": "sub-04",
+          "session_id": "ses-01",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/PhenotypicSession",
+          "age": 21.1,
+          "sex": "http://purl.bioontology.org/ontology/SNOMEDCT/248152002",
+          "diagnosis": [
+            null
+          ],
+          "subject_group": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C94342",
+          "assessment": [
+            "https://www.cognitiveatlas.org/task/id/tsk_4a57abb949ece"
+          ],
+          "image_modal": [
+            null
+          ],
+          "session_file_path": null
+        },
+        {
+          "sub_id": "sub-04",
+          "session_id": "ses-02",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/ImagingSession",
+          "age": null,
+          "sex": null,
+          "diagnosis": [
+            null
+          ],
+          "subject_group": null,
+          "assessment": [
+            null
+          ],
+          "image_modal": [
+            "http://purl.org/nidash/nidm#T1Weighted",
+            "http://purl.org/nidash/nidm#FlowWeighted"
+          ],
+          "session_file_path": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-02"
+        },
+        {
+          "sub_id": "sub-04",
+          "session_id": "ses-02",
+          "num_matching_phenotypic_sessions": 2,
+          "num_matching_imaging_sessions": 2,
+          "session_type": "http://neurobagel.org/vocab/PhenotypicSession",
+          "age": 22.3,
+          "sex": "http://purl.bioontology.org/ontology/SNOMEDCT/248152002",
+          "diagnosis": [
+            null
+          ],
+          "subject_group": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C94342",
+          "assessment": [
+            "https://www.cognitiveatlas.org/task/id/trm_57964b8a66aed",
+            "https://www.cognitiveatlas.org/task/id/tsk_4a57abb949ece"
+          ],
+          "image_modal": [
+            null
+          ],
+          "session_file_path": null
+        }
+      ],
+      "image_modals": [
+        "http://purl.org/nidash/nidm#T1Weighted",
+        "http://purl.org/nidash/nidm#FlowWeighted"
+      ]
+    }
+  ],
+  "nodes_response_status": "success"
+}

api-responses/make_api_responses.sh

@@ -0,0 +1,66 @@
+# The following script sets up two test nodes,
+# Test node 1: 2 OpenNeuro datasets, in the aggregate results mode
+# Test node 2: the (default) BIDS Synthetic dataset, in the unaggregated results mode
+#
+# A full_stack deployment recipe will be used for Test node 1 to provide local federation.
+
+mkdir test_node1 test_node2 api-responses
+
+# SETUP FOR TEST NODE 1
+git clone https://github.com/neurobagel/recipes.git test_node1/recipes
+
+# Get the data
+git clone https://github.com/neurobagel/openneuro-annotations.git test_node1/openneuro-annotations
+mkdir test_node1/openneuro_mini_data
+cp test_node1/openneuro-annotations/ds000001.jsonld test_node1/recipes/ds000002.jsonld test_node1/openneuro_mini_data
+
+cd test_node1/recipes
+cp template.env .env
+
+sed -i 's/^LOCAL_GRAPH_DATA=.*/LOCAL_GRAPH_DATA=../openneuro_mini_data/' .env
+sed -i 's/^NB_FEDERATE_REMOTE_PUBLIC_NODES=.*/NB_FEDERATE_REMOTE_PUBLIC_NODES=False/' .env
+sed -i 's/^NB_API_QUERY_URL=.*/NB_API_QUERY_URL=http://localhost:8080/' .env
+sed -i 's/^COMPOSE_PROFILES=.*/COMPOSE_PROFILES=full_stack/' .env
+
+# Use full container names to avoid conflicts
+echo '[{"NodeName": "2 OpenNeuro Datasets", "ApiURL": "http://neurobagel_node-api-1:8000"},{"NodeName": "BIDS Synthetic", "ApiURL": "http://neurobagel_node2-api-1:8000"}]' > local_nb_nodes.json
+
+# Generate a partial success result (since Test node 2 isn't up yet)
+docker compose up -d
+
+# WAIT FOR GRAPH TO FINISH BEING SET UP (?)
+while ! curl --silent "localhost:7200/rest/repositories" -u "DBUSER:DBPASSWORD" | grep '\['; do
+    :
+done
+
+# Query for female sex in f-API
+curl -s http://localhost:8080/query?sex=snomed:248152002 | jq .  > api-responses/fapi_query_partial_success_207.json
+
+# Generate a fail result (both nodes are not accessible)
+docker stop neurobagel_node-api-1
+curl -s http://localhost:8080/query?sex=snomed:248152002 | jq .  > api-responses/fapi_query_fail_207.json
+
+cd ../..
+
+# SETUP FOR TEST NODE 2
+git clone https://github.com/neurobagel/recipes.git test_node2/recipes
+cd test_node2/recipes
+cp template.env .env
+
+sed -i 's/^COMPOSE_PROJECT_NAME=.*/COMPOSE_PROJECT_NAME=neurobagel_node2/' .env
+sed -i 's/^NB_GRAPH_PORT_HOST=.*/NB_GRAPH_PORT_HOST=7201/' .env
+sed -i 's/^NB_NAPI_PORT_HOST=.*/NB_NAPI_PORT_HOST=8001/' .env
+
+# Generate a full success result (both nodes are running and accessible)
+# First, restart n-API for test node 1
+docker start neurobagel_node-api-1
+docker compose up -d
+# Add second n-API to the network of the first node, so that the f-API can access the second n-API by container name
+docker network add neurobagel_node_default neurobagel_node2-api-1
+curl -s http://localhost:8080/query?sex=snomed:248152002 | jq .  > api-responses/fapi_query_success_207.json
+
+
+# Generate query response where results are protected (test node 1)
+curl -s http://localhost:8000/query?sex=snomed:248152002 | jq . > api-responses/napi_query_aggregated_results.json
+# Generate query response where results are open (test node 2)
+curl -s http://localhost:8001/query?sex=snomed:248152002 | jq . > api-responses/napi_query_unaggregated_results.json

api-responses/napi_query_aggregated_results.json

@@ -0,0 +1,30 @@
+[
+  {
+    "dataset_uuid": "http://neurobagel.org/vocab/1c9a29d8-9ce7-4bb6-9c44-f33ac504bcb4",
+    "dataset_name": "Balloon Analog Risk-taking Task",
+    "dataset_portal_uri": "https://github.com/OpenNeuroDatasets-JSONLD/ds000001.git",
+    "dataset_total_subjects": 16,
+    "records_protected": true,
+    "num_matching_subjects": 10,
+    "subject_data": "protected",
+    "image_modals": [
+      "http://purl.org/nidash/nidm#T2Weighted",
+      "http://purl.org/nidash/nidm#T1Weighted",
+      "http://purl.org/nidash/nidm#FlowWeighted"
+    ]
+  },
+  {
+    "dataset_uuid": "http://neurobagel.org/vocab/c7bb6a5b-4066-4a59-b56c-3c6fe4d44b90",
+    "dataset_name": "Classification learning",
+    "dataset_portal_uri": "https://github.com/OpenNeuroDatasets-JSONLD/ds000002.git",
+    "dataset_total_subjects": 17,
+    "records_protected": true,
+    "num_matching_subjects": 10,
+    "subject_data": "protected",
+    "image_modals": [
+      "http://purl.org/nidash/nidm#T2Weighted",
+      "http://purl.org/nidash/nidm#T1Weighted",
+      "http://purl.org/nidash/nidm#FlowWeighted"
+    ]
+  }
+]