Fetch instances for types that can be used as funders from KG (HumanB…

…rainProject#11)
ehennestad · Feb 27, 2024 · 1e46c32 · 1e46c32
1 parent d58595c
commit 1e46c32
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Showing 2 changed files with 48 additions and 43 deletions.
diff --git a/server/kg-util/fetchCoreSchemaInstances.js b/server/kg-util/fetchCoreSchemaInstances.js
@@ -21,73 +21,68 @@ fs.mkdir(INSTANCE_OUTPUT_DIRECTORY, { recursive: true }, (err) => {
     }
 });
 
-// config instanceSpecification should contain the following properties:
-// - openMindsType // Rename to openMindsSchemaType e.g: "Person"
-// - instanceProperties // Rename to openMindsSchemaProperties
-// - space // Optional, defaults to "common"
-
-// Todo: Support array (list) input for instanceSpecification
-
-let fetchCoreSchemaInstances = async (instanceSpecification) => {
+// typeSpecification object should contain the following properties:
+// - openMindsType // short name for the openminds type, e.g: "Person"
+// - typeProperties // list of properties to save for this type, e.g: ["familyName", "givenName"]
+// - space // Optional, defaults to "common" (KG space to search for instances)
 
+let fetchCoreSchemaInstances = async (typeSpecifications) => {
     // Create request header with authorization and options
     const requestOptions = await getRequestOptions();
 
     return new Promise((resolve, reject) => {
-
+        
         // Define some api constants
         const API_BASE_URL = "https://core.kg.ebrains.eu/";
         const API_ENDPOINT = "v3/instances";
 
-        let spaceName = "common";
-        if (instanceSpecification.space != undefined) {
-            spaceName = instanceSpecification.space;
-        }
-
-        const QUERY_PARAMS = ["stage=RELEASED", `space=${spaceName}`, "type=https://openminds.ebrains.eu/core/"];
-
-        //const CORE_SCHEMAS = ["Person", "URL"]
-        const CORE_SCHEMAS = [instanceSpecification.openMindsType];
+        typeSpecifications.forEach(async (typeSpecification) => {
+            let spaceName = "common";
+            if (typeSpecification.space !== undefined) {
+                spaceName = typeSpecification.space;
+            }
 
-        // Loop through core schemas terms and fetch their instances
-        for (let i = 0; i < CORE_SCHEMAS.length; i++){
+            const QUERY_PARAMS = ["stage=RELEASED", `space=${spaceName}`, "type=https://openminds.ebrains.eu/core/"];
+            const TYPE_NAME = typeSpecification.openMindsType;
 
             // Assemble Query URL
-            let queryUrl = API_BASE_URL + API_ENDPOINT + "?" + QUERY_PARAMS.join("&") + CORE_SCHEMAS[i];
-            let instanceName = CORE_SCHEMAS[i];
-
-            // Fetch instances
-            fetchInstance(queryUrl, requestOptions, instanceName, instanceSpecification.instanceProperties)
-            .then( (data) => resolve(data) )
-            .catch( (error) => reject(error) )
-        }
+            let queryUrl = `${API_BASE_URL}${API_ENDPOINT}?${QUERY_PARAMS.join("&")}${TYPE_NAME}`;
+
+            try {
+                // Fetch instances
+                const data = await fetchInstances(queryUrl, requestOptions, TYPE_NAME, typeSpecification.typeProperties);
+                resolve(data);
+            } catch (error) {
+                reject(error);
+            }
+        });
     });
 }
 
 // function to get schema instances from kg api
-function fetchInstance(apiQueryUrl, requestOptions, instanceName, propertyNames) {
+function fetchInstances(apiQueryUrl, requestOptions, typeName, propertyNames) {
 
     return new Promise((resolve, reject) => {
         fetch(apiQueryUrl, requestOptions)
             .then( response => {
                 if (response.status===200) {
                     return response.json() 
                 } else {
-                    console.log('Error fetching instances for ' + instanceName + '. Status code: ' + response.status);
-                    throw new Error('Error fetching instances for ' + instanceName + '. Status code: ' + response.status)
+                    console.log('Error fetching instances for ' + typeName + '. Status code: ' + response.status);
+                    throw new Error('Error fetching instances for ' + typeName + '. Status code: ' + response.status)
                     reject()
                 }
                 }) // Get response promise
-                .then( data => parseAndSaveData(data, instanceName, propertyNames).then( (instances) => resolve(instances) ) )
+                .then( data => parseAndSaveData(data, typeName, propertyNames).then( (instances) => resolve(instances) ) )
                 .catch( error => {reject(error); console.log(error) } )
     });
 }
 
 // Parse and save schema instances
-function parseAndSaveData(data, instanceName, propertyNameList) {
+function parseAndSaveData(data, typeName, propertyNameList) {
     return new Promise((resolve, reject) => {
 
-        const schemaInstanceList = [];
+        const typeInstanceList = [];
 
         for (let thisInstance of data.data){
             let newInstance = {"identifier": thisInstance["@id"]};
@@ -98,21 +93,21 @@ function parseAndSaveData(data, instanceName, propertyNameList) {
                     newInstance[propertyNameList[i]] = thisInstance[vocabName];
                 }
             }
-            schemaInstanceList.push( newInstance );       
+            typeInstanceList.push( newInstance );       
         }
 
         // Save results to json file
-        const jsonStr = JSON.stringify(schemaInstanceList, null, 2);
+        const jsonStr = JSON.stringify(typeInstanceList, null, 2);
 
-        const filename = instanceName + '.json';
+        const filename = typeName + '.json';
         const filePath = path.join(INSTANCE_OUTPUT_DIRECTORY, filename);
 
         fs.writeFile(filePath, jsonStr, (err) => {
             if (err) {
                 console.error(err);
                 reject(err)
             } else {
-                console.log('File with instances for ' + instanceName + ' written successfully');
+                console.log('File with instances for ' + typeName + ' written successfully');
                 resolve()
             }
         });

diff --git a/setup.js b/setup.js
@@ -15,14 +15,24 @@ async function setup() {
 
     var startTime = performance.now()
 
-    configObject = {
-        openMindsType: "Person",
-        instanceProperties: ["familyName", "givenName"]
-    }
+    configObject = [
+        {
+            openMindsType: "Person",
+            typeProperties: ["familyName", "givenName"]
+        },
+        {
+            openMindsType: "Organization",
+            typeProperties: ["fullName"]
+        },
+        {
+            openMindsType: "Consortium",
+            typeProperties: ["fullName"]
+        },
+    ]
     // Temporary to retrieve strains for the workbench:
     // configObject = {
     //     openMindsType: "Strain",
-    //     instanceProperties: ["name", "description"],
+    //     typeProperties: ["name", "description"],
     //     space: "dataset"
     // }