Merge pull request #216 from PEM-Humboldt/release/1.9.0

Release 1.9.0
PEM-Humboldt · Aug 26, 2021 · 0350f0b · 0350f0b
2 parents 7a8d047 + 9ca4804
commit 0350f0b
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Showing 4 changed files with 127 additions and 129 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "biomodelos-api",
-  "version": "1.8.0",
+  "version": "1.9.0",
   "description": "RESTful server API for Biomodels.",
   "main": "index.js",
   "author": "Valentina Grajales Olarte - https://github.com/valegrajales",

diff --git a/src/api/models/model.controller.js b/src/api/models/model.controller.js
@@ -104,10 +104,17 @@ export async function read(req, res) {
         'Published',
         {
           taxID: req.params.taxID,
-          isActive: true,
           published: true,
           isActive: true
         }
+      ],
+      [
+        'Statistic',
+        {
+          taxID: req.params.taxID,
+          modelStatus: { $in: ['Statistic'] },
+          isActive: true
+        }
       ]
     ]);
     try {
@@ -664,9 +671,11 @@ export async function occurrenceCoversStatsModel(req, res) {
  *                 type: number
  *               validModels:
  *                 type: number
+ *               publishedModels:
+ *                 type: number
  *               developingModels:
  *                 type: number
- *               pendingValidation:
+ *               statisticModels:
  *                 type: number
  *             features:
  *               type: array
@@ -678,132 +687,125 @@ export async function occurrenceCoversStatsModel(req, res) {
  *         $ref: "#/definitions/ErrorResponse"
  */
 export async function generalModelStats(req, res) {
-  const totalStats: Array<{
-    taxonomicGroup: string,
-    totalSpecies: number,
-    developingModels?: number,
-    validModels?: number,
-    pendingValidation?: number
-  }> = [
-    {
-      taxonomicGroup: 'mamiferos',
-      totalSpecies: 492
-    },
-    { taxonomicGroup: 'aves', totalSpecies: 1921 },
-    { taxonomicGroup: 'reptiles', totalSpecies: 537 },
-    { taxonomicGroup: 'anfibios', totalSpecies: 803 },
-    { taxonomicGroup: 'peces', totalSpecies: 1435 },
-    { taxonomicGroup: 'invertebrados', totalSpecies: 19312 },
-    { taxonomicGroup: 'plantas', totalSpecies: 22840 }
-  ];
+  let groups = [];
   try {
-    const docs = await Specie.aggregate([
+    groups = await Specie.aggregate([
       {
-        $match: {
-          $and: [
-            {
-              $or: [
-                {
-                  bmClass: {
-                    $in: [
-                      'mamiferos',
-                      'aves',
-                      'reptiles',
-                      'anfibios',
-                      'peces',
-                      'invertebrados',
-                      'plantas'
-                    ]
-                  }
-                }
-              ]
-            }
-          ]
+        $group: {
+          _id: {
+            taxonomyClass: '$bmClass'
+          },
+          taxes: { $push: '$taxID' },
+          total: { $sum: 1 }
         }
-      },
+      }
+    ]);
+  } catch (err) {
+    log.error(err);
+    res.send('There was an error getting the statistics');
+  }
+
+  const stats = groups.map(group =>
+    Model.aggregate([
       {
-        $lookup: {
-          localField: 'taxID',
-          from: 'models',
-          foreignField: 'taxID',
-          as: 'models'
+        $match: {
+          taxID: { $in: group.taxes },
+          isActive: true,
+          modelLevel: 1
         }
       },
-      { $unwind: '$models' },
       {
-        $match: {
-          $and: [
-            { 'models.isActive': { $in: [true] } },
-            { 'models.modelLevel': { $in: [1] } }
-          ]
+        $project: {
+          taxID: 1,
+          status: {
+            $switch: {
+              branches: [
+                {
+                  case: { $eq: ['$modelStatus', 'Valid'] },
+                  then: '0-Valid'
+                },
+                {
+                  case: {
+                    $and: [
+                      { $eq: ['$modelStatus', 'pendingValidation'] },
+                      { $eq: ['$published', true] }
+                    ]
+                  },
+                  then: '1-Published'
+                },
+                {
+                  case: { $eq: ['$modelStatus', 'pendingValidation'] },
+                  then: '2-Developing'
+                },
+                {
+                  case: { $eq: ['$modelStatus', 'Statistic'] },
+                  then: '3-Statistic'
+                }
+              ],
+              default: '4-no-model'
+            }
+          }
         }
       },
+      { $sort: { status: 1 } },
       {
         $group: {
           _id: {
-            taxonomyClass: '$bmClass',
-            modelStatus: '$models.modelStatus',
             taxID: '$taxID'
           },
-          count: { $sum: 1 }
+          modelStatus: { $first: '$status' }
         }
       },
-      {
-        $group: {
-          _id: { taxonomyClass: '$_id.taxonomyClass', taxID: '$_id.taxID' },
-          modelStatus: {
-            $push: { status: '$_id.modelStatus', count: '$count' }
-          }
-        }
-      },
-      { $unwind: '$modelStatus' },
-      {
-        $sort: { 'modelStatus.status': -1 }
-      },
-      { $group: { _id: '$_id', modelStatus: { $first: '$modelStatus' } } },
       {
         $group: {
           _id: {
-            taxonomyClass: '$_id.taxonomyClass',
-            modelStatus: '$modelStatus.status'
+            modelStatus: '$modelStatus'
           },
           count: { $sum: 1 }
         }
       },
       {
-        $group: {
-          _id: '$_id.taxonomyClass',
-          modelStatus: {
-            $push: { status: '$_id.modelStatus', count: '$count' }
-          }
+        $project: {
+          modelStatus: '$_id.modelStatus',
+          count: 1,
+          _id: 0
         }
       }
-    ]);
-    docs.map(elem => {
-      const obj = totalStats.find(x => x.taxonomicGroup === elem._id);
-      const index = totalStats.indexOf(obj);
-      elem.modelStatus.map(elem => {
-        switch (elem.status) {
-          case 'Developing':
-            // eslint-disable-next-line security/detect-object-injection
-            totalStats[index].developingModels = elem.count;
-            break;
-          case 'Valid':
-            // eslint-disable-next-line security/detect-object-injection
-            totalStats[index].validModels = elem.count;
-            break;
-          case 'pendingValidation':
-            // eslint-disable-next-line security/detect-object-injection
-            totalStats[index].pendingValidation = elem.count;
-            break;
-        }
+    ])
+  );
+
+  return Promise.all(stats)
+    .then(response => {
+      const result = groups.map((group, index) => {
+        /* eslint-disable security/detect-object-injection */
+        const validModels = response[index].find(
+          e => e.modelStatus === '0-Valid'
+        );
+        const publishedModels = response[index].find(
+          e => e.modelStatus === '1-Published'
+        );
+        const developingModels = response[index].find(
+          e => e.modelStatus === '2-Developing'
+        );
+        const statisticModels = response[index].find(
+          e => e.modelStatus === '3-Statistic'
+        );
+        /* eslint-enable security/detect-object-injection */
+        return {
+          taxonomicGroup: group._id.taxonomyClass,
+          totalSpecies: group.total,
+          validModels: validModels ? validModels.count : 0,
+          publishedModels: publishedModels ? publishedModels.count : 0,
+          developingModels: developingModels ? developingModels.count : 0,
+          statisticModels: statisticModels ? statisticModels.count : 0
+        };
       });
+      res.json(result);
+    })
+    .catch(err => {
+      log.error(err);
+      res.send('There was an error getting the statistics');
     });
-    res.json(totalStats);
-  } catch (err) {
-    log.error(err);
-    res.send('There was an error getting the statistics');
-  }
 }
 
 /**

diff --git a/src/api/species/specie.controller.js b/src/api/species/specie.controller.js
@@ -1,5 +1,6 @@
 import GeoJSON from 'geojson';
 import { Record } from '../../models/record.model';
+import Model from '../../models/model.model';
 import Specie from '../../models/specie.model';
 const log = require('../../config/log').logger();
 
@@ -321,31 +322,7 @@ export async function getAllSpecies(req, res) {
   const query = constructQuery(req);
   try {
     let docs = [];
-    if (req.query.modelStatus) {
-      docs = await Specie.aggregate([
-        {
-          $match: query
-        },
-        {
-          $lookup: {
-            localField: 'taxID',
-            from: 'models',
-            foreignField: 'taxID',
-            as: 'models'
-          }
-        },
-        {
-          $match: { 'models.modelStatus': req.query.modelStatus }
-        },
-        {
-          $project: {
-            species: 1,
-            taxID: 1,
-            _id: 0
-          }
-        }
-      ]).sort({ species: 1 });
-    } else if (req.query.speciesIn) {
+    if (req.query.speciesIn) {
       docs = await Specie.aggregate([
         {
           $match: {
@@ -368,7 +345,26 @@ export async function getAllSpecies(req, res) {
         { $sort: { acceptedNameUsage: 1 } }
       ]);
     } else {
-      docs = await Specie.find(query, {
+      let modelsFilter = {};
+      if (req.query.modelStatus) {
+        const taxIds = await Model.find(
+          { modelStatus: req.query.modelStatus, isActive: true },
+          { taxID: 1, _id: 0 }
+        );
+        modelsFilter = {
+          taxID: {
+            $in: taxIds.map(e => e.taxID)
+          }
+        };
+      } else if (!!req.query.withModel) {
+        const taxIds = await Model.distinct('taxID', { isActive: true });
+        modelsFilter = {
+          taxID: {
+            $in: taxIds
+          }
+        };
+      }
+      docs = await Specie.find(Object.assign(query, modelsFilter), {
         species: 1,
         taxID: 1,
         _id: 0
@@ -523,7 +519,7 @@ export async function searchSpecies(req, res) {
     fullAccess = scopes.includes('all');
   }
 
-  let project = { _id: 0, species: 1, taxID: 1 }
+  let project = { _id: 0, species: 1, taxID: 1 };
   if (fullAccess) {
     project = {
       _id: 0,