Merge branch 'dev' of github.com:haniffalab/strapi-api into dev

davehorsfall · davehorsfall · commit 69fa31efe3a9 · 2025-04-01T11:02:24.000+01:00
diff --git a/.github/workflows/deploy-appengine-dev.yml b/.github/workflows/deploy-appengine-dev.yml
@@ -30,6 +30,7 @@ jobs:
       GCS_PUBLIC_FILES: ${{ secrets.GCS_PUBLIC_FILES }}
       GCS_UNIFORM: ${{ secrets.GCS_UNIFORM }}
       GCS_SERVICE_ACCOUNT: ${{ secrets.GCP_SA_KEY }}
+      SENDGRID_API_KEY: ${{ secrets.SENDGRID_API_KEY }}
 
     steps:
       - uses: actions/checkout@v3
diff --git a/.github/workflows/deploy-appengine.yml b/.github/workflows/deploy-appengine.yml
@@ -30,6 +30,7 @@ jobs:
       GCS_PUBLIC_FILES: ${{ secrets.GCS_PUBLIC_FILES }}
       GCS_UNIFORM: ${{ secrets.GCS_UNIFORM }}
       GCS_SERVICE_ACCOUNT: ${{ secrets.GCP_SA_KEY }}
+      SENDGRID_API_KEY: ${{ secrets.SENDGRID_API_KEY }}
 
     steps:
       - uses: actions/checkout@v3
diff --git a/create_yaml.sh b/create_yaml.sh
@@ -22,6 +22,7 @@ env_variables:
   GCS_PUBLIC_FILES: $GCS_PUBLIC_FILES
   GCS_UNIFORM: $GCS_UNIFORM
   GCS_SERVICE_ACCOUNT: '$GCS_SERVICE_ACCOUNT'
+  SENDGRID_API_KEY: $SENDGRID_API_KEY
 automatic_scaling:
   min_instances: $MIN_INSTANCES
   max_instances: $MAX_INSTANCES
diff --git a/src/api/collection/content-types/collection/lifecycles.js b/src/api/collection/content-types/collection/lifecycles.js
@@ -0,0 +1,29 @@
+module.exports = {
+  async beforeCreate(event) {
+    event.params.data.uid = await strapi.service('plugin::content-manager.uid')
+      .generateUIDField({
+        contentTypeUID: 'api::collection.collection',
+        field: 'uid',
+        data: event.params.data
+      });
+  },
+  async beforeUpdate(event) {
+    const { data, where } = event.params;
+
+    const isPublishAction = 'publishedAt' in data;
+
+    if (!isPublishAction){
+      const entry = await strapi.entityService.findOne('api::collection.collection', where.id);
+
+      if ('name' in data && data.name !== entry.name){
+        event.params.data.uid = await strapi.service('plugin::content-manager.uid')
+          .generateUIDField({
+            contentTypeUID: 'api::collection.collection',
+            field: 'uid',
+            data: data
+          });
+      }
+    }
+  },
+
+};
diff --git a/src/api/collection/content-types/collection/schema.json b/src/api/collection/content-types/collection/schema.json
@@ -27,7 +27,13 @@
     },
     "name": {
       "type": "string",
-      "unique": true
+      "unique": true,
+      "required": true
+    },
+    "uid": {
+      "type": "uid",
+      "targetField": "name",
+      "required": true
     }
   }
 }
diff --git a/src/api/collection/services/collection.js b/src/api/collection/services/collection.js
@@ -6,4 +6,24 @@
 
 const { createCoreService } = require('@strapi/strapi').factories;
 
-module.exports = createCoreService('api::collection.collection');
+module.exports = createCoreService('api::collection.collection', ({strapi}) => ({
+  async findByUid(ctx){
+    const ctUid = 'api::collection.collection';
+    const attrs = strapi.contentTypes[ctUid].__schema__.attributes;
+    const uidTarget =attrs['uid'].targetField;
+    const { [uidTarget]: uidTargetValue } = ctx.params;
+    
+    const populateParams = strapi.config.functions.getPopulateParams(attrs);
+    
+    let entity = await strapi.db.query(ctUid).findOne({
+      where: { [uidTarget]: uidTargetValue },
+      populate: populateParams
+    });
+
+    if (entity){
+      entity = strapi.config.functions.reduceComponentData(attrs, entity);
+    }
+
+    return entity;
+  }
+}));
diff --git a/src/api/dataset/content-types/dataset/lifecycles.js b/src/api/dataset/content-types/dataset/lifecycles.js
@@ -1,28 +1,37 @@
 module.exports = {
   async beforeCreate(event) {
-    event.params.data.uid = await strapi.service('plugin::content-manager.uid')
+    const { data } = event.params;
+
+    const uid = await strapi.service('plugin::content-manager.uid')
       .generateUIDField({
         contentTypeUID: 'api::dataset.dataset',
         field: 'uid',
-        data: event.params.data
+        data: event.params.data.name
       });
+
+    event.params.data.uid = uid;
+    event.params.data.dataset_id = (data.study?.connect?.[0]?.id || null) + ':' + uid;
   },
   async beforeUpdate(event) {
     const { data, where } = event.params;
 
     const isPublishAction = 'publishedAt' in data;
 
     if (!isPublishAction){
-      const entry = await strapi.entityService.findOne('api::dataset.dataset', where.id);
-    
+      const entry = await strapi.entityService.findOne('api::dataset.dataset', where.id,
+        {populate: {study: {fields: ['id']}}}
+      );
+
       if ('name' in data && data.name !== entry.name){
         event.params.data.uid = await strapi.service('plugin::content-manager.uid')
           .generateUIDField({
             contentTypeUID: 'api::dataset.dataset',
             field: 'uid',
-            data: data
+            data: data.name
           });
       }
+
+      event.params.data.dataset_id = (data.study?.connect?.[0] || entry.study?.id || null) + ':' + (event.params.data.uid || entry.uid);
     }
   },
 };
diff --git a/src/api/dataset/content-types/dataset/schema.json b/src/api/dataset/content-types/dataset/schema.json
@@ -23,7 +23,7 @@
     "name": {
       "type": "string",
       "required": true,
-      "unique": true
+      "unique": false
     },
     "description": {
       "type": "text"
@@ -59,7 +59,7 @@
     },
     "uid": {
       "type": "uid",
-      "targetField": "name",
+      "targetField": "dataset_id",
       "required": true
     },
     "metadata": {
@@ -120,6 +120,15 @@
         "ontology": "hsapdv"
       },
       "customField": "plugin::ebi-ols.ontology-term"
+    },
+    "resources": {
+      "type": "component",
+      "repeatable": true,
+      "component": "data.resource"
+    },
+    "dataset_id": {
+      "type": "string",
+      "unique": true
     }
   }
 }
diff --git a/src/api/dataset/controllers/dataset.js b/src/api/dataset/controllers/dataset.js
@@ -41,8 +41,11 @@ module.exports = createCoreController('api::dataset.dataset', ({ strapi }) => ({
           fields: ['name', 'slug'],
         },
         data: {
-          fields: ['format', 'file_type']
+          fields: ['type']
         },
+        resources: {
+          fields: ['name', 'description', 'type', 'category', 'is_primary_data']
+        }
       }
     };
     return await super.find(ctx);
@@ -60,6 +63,7 @@ module.exports = createCoreController('api::dataset.dataset', ({ strapi }) => ({
           fields: ['name', 'slug'],
         },
         data: true,
+        resources: true,
       }
     };
     const dataset = await super.findOne(ctx);
diff --git a/src/api/dataset/services/dataset.js b/src/api/dataset/services/dataset.js
@@ -10,13 +10,21 @@ module.exports = createCoreService('api::dataset.dataset', ({strapi}) => ({
   async findByUid(ctx){
     const ctUid = 'api::dataset.dataset';
     const attrs = strapi.contentTypes[ctUid].__schema__.attributes;
-    const uidTarget =attrs['uid'].targetField;
-    const { [uidTarget]: uidTargetValue } = ctx.params;
-    
+    const { dataset_id, name, study_id } = ctx.params;
+
+    let where;
+    if (dataset_id){
+      where = { dataset_id: dataset_id };
+    }
+    else {
+      const studyEntry = await strapi.service('api::study.study').findByUid({params: {study_id: study_id}});
+      where = { study: studyEntry?.id || null, name: name };
+    }
+
     const populateParams = strapi.config.functions.getPopulateParams(attrs);
-    
+ 
     let entity = await strapi.db.query(ctUid).findOne({
-      where: { [uidTarget]: uidTargetValue },
+      where: where,
       populate: populateParams
     });
 
diff --git a/src/api/study/content-types/study/lifecycles.js b/src/api/study/content-types/study/lifecycles.js
@@ -13,6 +13,8 @@ module.exports = {
     event.params.data.password = data.password?.length ?
       bcrypt.hashSync(data.password, 10) :
       null;
+
+    event.state = data.datasets;
   },
   async beforeUpdate(event) {
     const { data, where } = event.params;
@@ -37,5 +39,29 @@ module.exports = {
           null;
       }
     }
+
+    event.state = data.datasets;
+  },
+  // Update datasets' dataset_id when connecting/disconnecting to/from study
+  async afterCreate(event) {
+    const datasets = event.state;
+    for (const idx in datasets) {
+      await strapi.entityService.update('api::dataset.dataset', datasets[idx], {
+        data: { study: event.result.id }
+      });
+    }
   },
+  async afterUpdate(event) {
+    const { disconnect, connect } = event.state;
+    for (const idx in disconnect) {
+      await strapi.entityService.update('api::dataset.dataset', disconnect[idx].id, {
+        data: { study: null }
+      });
+    }
+    for (const idx in connect) {
+      await strapi.entityService.update('api::dataset.dataset', connect[idx].id, {
+        data: { study: event.result.id }
+      });
+    }
+  }
 };
diff --git a/src/api/study/content-types/study/schema.json b/src/api/study/content-types/study/schema.json
@@ -98,6 +98,11 @@
       "type": "customField",
       "customField": "plugin::custom-fields.customPassword",
       "private": true
+    },
+    "resources": {
+      "type": "component",
+      "repeatable": true,
+      "component": "data.resource"
     }
   }
 }
diff --git a/src/api/study/controllers/study.js b/src/api/study/controllers/study.js
@@ -43,7 +43,7 @@ module.exports = createCoreController('api::study.study', ({ strapi }) => ({
       populate: {
         cover_image: true,
         publications: {
-          fields: ['title', 'doi', 'url', 'abstract'],
+          fields: ['title', 'doi', 'url', 'abstract', 'date', 'is_published', 'is_preprint'],
           populate: {
             journal: {
               fields: ['name'],
@@ -73,6 +73,9 @@ module.exports = createCoreController('api::study.study', ({ strapi }) => ({
           fields: ['name', 'description', 'tissues', 'organisms', 'assays', 'diseases', 'celltypes', 'human_developmental_stages', 'count'],
           populate: ['media'],
         },
+        resources: {
+          fields: ['name', 'description', 'type', 'category' ]
+        }
       },
     };
     return await super.find(ctx);
@@ -96,7 +99,7 @@ module.exports = createCoreController('api::study.study', ({ strapi }) => ({
       populate: {
         cover_image: true,
         publications: {
-          fields: ['title', 'doi', 'url', 'abstract'],
+          fields: ['title', 'doi', 'url', 'abstract', 'date', 'is_published', 'is_preprint'],
           populate: {
             journal: {
               fields: ['name'],
@@ -124,8 +127,9 @@ module.exports = createCoreController('api::study.study', ({ strapi }) => ({
         },
         datasets: {
           fields: ['name', 'description', 'tissues', 'organisms', 'assays', 'diseases', 'celltypes', 'human_developmental_stages', 'count'],
-          populate: ['media'],
+          populate: ['media', 'data', 'resources'],
         },
+        resources: true
       },
     };
 
diff --git a/src/api/team/content-types/team/lifecycles.js b/src/api/team/content-types/team/lifecycles.js
@@ -0,0 +1,28 @@
+module.exports = {
+  async beforeCreate(event) {
+    event.params.data.uid = await strapi.service('plugin::content-manager.uid')
+      .generateUIDField({
+        contentTypeUID: 'api::team.team',
+        field: 'uid',
+        data: event.params.data
+      });
+  },
+  async beforeUpdate(event) {
+    const { data, where } = event.params;
+
+    const isPublishAction = 'publishedAt' in data;
+
+    if (!isPublishAction){
+      const entry = await strapi.entityService.findOne('api::team.team', where.id);
+    
+      if ('name' in data && data.name !== entry.name){
+        event.params.data.uid = await strapi.service('plugin::content-manager.uid')
+          .generateUIDField({
+            contentTypeUID: 'api::team.team',
+            field: 'uid',
+            data: data
+          });
+      }
+    }
+  },
+};
diff --git a/src/api/team/content-types/team/schema.json b/src/api/team/content-types/team/schema.json
@@ -21,7 +21,9 @@
       "configurable": false
     },
     "name": {
-      "type": "string"
+      "type": "string",
+      "unique": true,
+      "required": true
     },
     "logo": {
       "type": "media",
@@ -42,6 +44,11 @@
     },
     "email": {
       "type": "email"
+    },
+    "uid": {
+      "type": "uid",
+      "targetField": "name",
+      "required": true
     }
   }
 }
diff --git a/src/api/team/services/team.js b/src/api/team/services/team.js
@@ -6,4 +6,24 @@
 
 const { createCoreService } = require('@strapi/strapi').factories;
 
-module.exports = createCoreService('api::team.team');
+module.exports = createCoreService('api::team.team', ({strapi}) => ({
+  async findByUid(ctx){
+    const ctUid = 'api::team.team';
+    const attrs = strapi.contentTypes[ctUid].__schema__.attributes;
+    const uidTarget =attrs['uid'].targetField;
+    const { [uidTarget]: uidTargetValue } = ctx.params;
+    
+    const populateParams = strapi.config.functions.getPopulateParams(attrs);
+    
+    let entity = await strapi.db.query(ctUid).findOne({
+      where: { [uidTarget]: uidTargetValue },
+      populate: populateParams
+    });
+
+    if (entity){
+      entity = strapi.config.functions.reduceComponentData(attrs, entity);
+    }
+
+    return entity;
+  }
+}));
diff --git a/src/components/data/file.json b/src/components/data/file.json
diff --git a/src/components/data/resource.json b/src/components/data/resource.json
diff --git a/src/plugins/data-import/README.md b/src/plugins/data-import/README.md
diff --git a/src/plugins/data-import/server/content-types/datafile/import.js b/src/plugins/data-import/server/content-types/datafile/import.js
diff --git a/src/plugins/data-import/server/content-types/datafile/validation.js b/src/plugins/data-import/server/content-types/datafile/validation.js

Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,13 @@`
`27`	`27`	`},`
`28`	`28`	`"name": {`
`29`	`29`	`"type": "string",`
`30`		`- "unique": true`
	`30`	`+ "unique": true,`
	`31`	`+ "required": true`
	`32`	`+ },`
	`33`	`+ "uid": {`
	`34`	`+ "type": "uid",`
	`35`	`+ "targetField": "name",`
	`36`	`+ "required": true`
`31`	`37`	`}`
`32`	`38`	`}`
`33`	`39`	`}`