Merge pull request #44 from haniffalab/feat/resources

davehorsfall · web-flow · commit 2b1f541e8441 · 2025-03-28T11:56:27.000Z
Feat/resources
diff --git a/src/api/collection/content-types/collection/schema.json b/src/api/collection/content-types/collection/schema.json
@@ -27,7 +27,8 @@
     },
     "name": {
       "type": "string",
-      "unique": true
+      "unique": true,
+      "required": true
     },
     "uid": {
       "type": "uid",
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] || 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/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",
diff --git a/src/components/data/file.json b/src/components/data/file.json
@@ -6,48 +6,19 @@
   },
   "options": {},
   "attributes": {
-    "file_type": {
-      "type": "enumeration",
-      "enum": [
-        "h5ad",
-        "h5",
-        "h5mu",
-        "zarr",
-        "tif",
-        "zip",
-        "h5seurat",
-        "rds",
-        "csv",
-        "txt",
-        "xlsx",
-        "json",
-        "link",
-        "other"
-      ]
-    },
     "url": {
       "type": "string"
     },
-    "format": {
+    "metadata": {
+      "type": "json"
+    },
+    "type": {
       "type": "enumeration",
       "enum": [
-        "AnnData",
-        "Seurat",
-        "MuData",
-        "SpatialData",
-        "Raw OME-TIFF",
-        "Label OME-TIFF",
-        "OME-TIFF",
-        "CellRanger",
-        "SpaceRanger",
-        "WebAtlas config",
-        "metadata",
-        "other"
+        "AnnData-Zarr",
+        "VitessceConfig"
       ],
       "required": true
-    },
-    "metadata": {
-      "type": "json"
     }
   }
 }
diff --git a/src/components/data/resource.json b/src/components/data/resource.json
@@ -0,0 +1,41 @@
+{
+  "collectionName": "components_data_resources",
+  "info": {
+    "displayName": "resource",
+    "description": ""
+  },
+  "options": {},
+  "attributes": {
+    "name": {
+      "type": "string",
+      "required": true
+    },
+    "description": {
+      "type": "text"
+    },
+    "url": {
+      "type": "string"
+    },
+    "type": {
+      "type": "enumeration",
+      "enum": [
+        "link",
+        "file"
+      ],
+      "default": "link",
+      "required": true
+    },
+    "is_primary_data": {
+      "type": "boolean",
+      "default": false
+    },
+    "category": {
+      "type": "enumeration",
+      "enum": [
+        "repository",
+        "other"
+      ],
+      "default": "other"
+    }
+  }
+}
diff --git a/src/plugins/data-import/README.md b/src/plugins/data-import/README.md
@@ -60,7 +60,7 @@ In order to make the JSON more user-friendly, the plugin doesn't expect the user
 
 For this to work the plugin expects the content-type to contain a `uid` attribute that has as `target` the field that should be used as an identifier. For example, The `uid` of the `dataset` content-type has the `name` field as its `target`. The value of the `uid` field itself is irrelevant, it is only used as a flag to indicate the field used as identifier. The motivation for this approach is to have non-numerical identifiers that are not limited to slug-like text (can contain spaces, etc.) Of course this also means that if the text doesn't match **exactly** then another entry will be created instead of updated. To remove emphasis on the `uid` fields the content-types are expected to make them non-configurable from the admin UI and automatically generate them in lifecycle hooks using the `strapi.service('plugin::content-manager.uid').generateUIDField` function.
 
-**Note** the `person` and `disease_gene` content-type need additional setup. `person` contains `first_name` and `last_name` fields which by themselves are not useful as unique identifiers. For that reason the `person` model uses a `full_name` field which is non-configurable through the admin UI and generated from the `first_name` and `last_name` fields in its lifecycle hooks. This `full_name` field is then used as the `uid` field's target. `disease_gene` contains `gene_id` and `disease_id` fields which are automatically used to set a `disease_gene` field which is the `uid` field's target.
+**Note** the `dataset`, `person` and `disease_gene` content-type need additional setup. `dataset` has a `dataset_id` unique field that is automatically generated from the dataset `uid` (also automatically generated) and the related `study`'s `id` (if any or `null`) This is to support datasets having same name but different study, instead of enforcing a unique name across all datasets. A `dataset` update through the plugin should be through a file that specifies the `dataset`'s `name` and related `study_id` (even if the study will be created in the import). `person` contains `first_name` and `last_name` fields which by themselves are not useful as unique identifiers. For that reason the `person` model uses a `full_name` field which is non-configurable through the admin UI and generated from the `first_name` and `last_name` fields in its lifecycle hooks. This `full_name` field is then used as the `uid` field's target. `disease_gene` contains `gene_id` and `disease_id` fields which are automatically used to set a `disease_gene` field which is the `uid` field's target.
 
 ### findByUid service
 
diff --git a/src/plugins/data-import/server/content-types/datafile/import.js b/src/plugins/data-import/server/content-types/datafile/import.js
@@ -56,9 +56,10 @@ const createOrUpdate = async (uid, entry, datafile_id, publish_on_import) => {
   entry.datafile = datafile_id;
 
   // Search for entry in database
-  const ctFields = Object.keys(attrs)
-    .filter((k) => attrs[k].type !== 'component');
-  const entityData = object.pick(entry, ctFields);
+  // keep all fields that are not component
+  const componentFields = Object.keys(attrs)
+    .filter((k) => attrs[k].type === 'component');
+  const entityData = object.omit(entry, componentFields);
 
   const data = await strapi.service(uid).findByUid({params: entityData})
     .catch((e) => { throw e; });
diff --git a/src/plugins/data-import/server/content-types/datafile/validation.js b/src/plugins/data-import/server/content-types/datafile/validation.js
@@ -71,11 +71,12 @@ const validateEntry = async (uid, entry, parents, is_component=false) => {
   }
 
   // Check if unrecognized fields are present
+  // log but don't throw error
   const unrecognized = array.difference(Object.keys(entry), Object.keys(attrs));
   if (unrecognized.length) {
     console.log('Unrecognized fields', parents.concat([unrecognized]));
-    throw new ValidationError('Unrecognized fields ' +
-      unrecognized + ' in ' + parents.join('>'));
+    // throw new ValidationError('Unrecognized fields ' +
+    //   unrecognized + ' in ' + parents.join('>'));
   }
 
   // Check all required fields are present

Original file line number	Diff line number	Diff line change
`@@ -98,6 +98,11 @@`
`98`	`98`	`"type": "customField",`
`99`	`99`	`"customField": "plugin::custom-fields.customPassword",`
`100`	`100`	`"private": true`
	`101`	`+ },`
	`102`	`+ "resources": {`
	`103`	`+ "type": "component",`
	`104`	`+ "repeatable": true,`
	`105`	`+ "component": "data.resource"`
`101`	`106`	`}`
`102`	`107`	`}`
`103`	`108`	`}`