From 3c2081f2805d8bc25b908bdfb351b83ef8d626de Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Mon, 20 Jun 2022 13:27:50 -0300
Subject: [PATCH 01/29] Add get example experiments endpoint

---
 .../controllers/experimentController.js       | 23 ++++++
 src/api.v2/helpers/roles.js                   |  4 +-
 src/api.v2/model/Experiment.js                | 19 +++--
 src/api.v2/routes/experiment.js               | 13 +++-
 src/specs/api.v2.yaml                         | 76 ++++++++++++++++++-
 ...iments.v2.yaml => ExperimentsList.v2.yaml} |  0
 6 files changed, 123 insertions(+), 12 deletions(-)
 rename src/specs/models/experiment-bodies/{GetAllExperiments.v2.yaml => ExperimentsList.v2.yaml} (100%)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 37d66863d..6e3791dee 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -19,6 +19,12 @@ const getAllExperiments = async (req, res) => {
   res.json(data);
 };
 
+const getAllExampleExperiments = async (req, res) => {
+  const data = await new Experiment().getAllExampleExperiments();
+
+  res.json(data);
+};
+
 const getExperiment = async (req, res) => {
   const { params: { experimentId } } = req;
 
@@ -129,11 +135,27 @@ const downloadData = async (req, res) => {
   logger.log(`Providing download link for download ${downloadType} for experiment ${experimentId}`);
 
   const downloadLink = await new Experiment().getDownloadLink(experimentId, downloadType);
+
+  logger.log(`Finished providing download link for download ${downloadType} for experiment ${experimentId}`);
   res.json(downloadLink);
 };
 
+const cloneExperiment = async (req, res) => {
+  const { experimentId } = req.params;
+
+  logger.log(`Cloning experiment ${experimentId}`);
+
+  const cloneExperimentId = await new Experiment().createClone(experimentId);
+  // const downloadLink = await new SampleFile().getDownloadLink(experimentId, downloadType);
+
+  logger.log(`Finished cloning experiment ${experimentId}, new expeirment's id is ${cloneExperimentId}`);
+
+  res.json(cloneExperimentId);
+};
+
 module.exports = {
   getAllExperiments,
+  getAllExampleExperiments,
   getExperiment,
   createExperiment,
   updateProcessingConfig,
@@ -143,4 +165,5 @@ module.exports = {
   getProcessingConfig,
   getBackendStatus,
   downloadData,
+  cloneExperiment,
 };
diff --git a/src/api.v2/helpers/roles.js b/src/api.v2/helpers/roles.js
index 0223105c1..084dd2f25 100644
--- a/src/api.v2/helpers/roles.js
+++ b/src/api.v2/helpers/roles.js
@@ -19,7 +19,9 @@ const allowedResources = {
     '/experiments/(?<experimentId>.*)/plots-tables/(?<plotUuid>.*)',
     '/experiments/(?<experimentId>.*)/cellSets',
   ],
-  [VIEWER]: [],
+  [VIEWER]: [
+    '/experiments/(?<experimentId>.*)/clone',
+  ],
 };
 const isRoleAuthorized = (role, resource, method) => {
   // if no valid role is provided, return not authorized
diff --git a/src/api.v2/model/Experiment.js b/src/api.v2/model/Experiment.js
index 139322ec2..107a93626 100644
--- a/src/api.v2/model/Experiment.js
+++ b/src/api.v2/model/Experiment.js
@@ -43,20 +43,27 @@ class Experiment extends BasicModel {
     ];
 
     const aliasedExperimentFields = fields.map((field) => `e.${field}`);
-    function mainQuery() {
-      this.select([...aliasedExperimentFields, 'm.key'])
+
+    const result = await collapseKeyIntoArray(
+      this.sql.select([...aliasedExperimentFields, 'm.key'])
         .from(tableNames.USER_ACCESS)
         .where('user_id', userId)
         .join(`${tableNames.EXPERIMENT} as e`, 'e.id', `${tableNames.USER_ACCESS}.experiment_id`)
         .leftJoin(`${tableNames.METADATA_TRACK} as m`, 'e.id', 'm.experiment_id')
-        .as('mainQuery');
-    }
-
-    const result = await collapseKeyIntoArray(mainQuery, [...fields], 'key', 'metadataKeys', this.sql);
+        .as('mainQuery'), [...fields],
+      'key',
+      'metadataKeys',
+      this.sql,
+    );
 
     return result;
   }
 
+  async getAllExampleExperiments() {
+    const noOwnerExperiments = '00000000-0000-0000-0000-000000000000';
+    return this.getAllExperiments(noOwnerExperiments);
+  }
+
   async getExperimentData(experimentId) {
     function mainQuery() {
       this.select('*')
diff --git a/src/api.v2/routes/experiment.js b/src/api.v2/routes/experiment.js
index c0696a75f..c2a99d07c 100644
--- a/src/api.v2/routes/experiment.js
+++ b/src/api.v2/routes/experiment.js
@@ -1,7 +1,8 @@
 const {
-  createExperiment, getExperiment, patchExperiment, deleteExperiment,
-  updateSamplePosition, getAllExperiments,
+  getAllExperiments, getAllExampleExperiments,
+  createExperiment, getExperiment, patchExperiment, deleteExperiment, cloneExperiment,
   getProcessingConfig, updateProcessingConfig,
+  updateSamplePosition,
   getBackendStatus, downloadData,
 } = require('../controllers/experimentController');
 
@@ -12,6 +13,10 @@ module.exports = {
     expressAuthenticationOnlyMiddleware,
     (req, res, next) => getAllExperiments(req, res).catch(next),
   ],
+  'experiment#getAllExampleExperiments': [
+    expressAuthenticationOnlyMiddleware,
+    (req, res, next) => getAllExampleExperiments(req, res).catch(next),
+  ],
   'experiment#getExperiment': [
     expressAuthorizationMiddleware,
     (req, res, next) => getExperiment(req, res).catch(next),
@@ -48,4 +53,8 @@ module.exports = {
     expressAuthorizationMiddleware,
     (req, res, next) => downloadData(req, res).catch(next),
   ],
+  'experiment#clone': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => cloneExperiment(req, res).catch(next),
+  ],
 };
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index 1c6f26fac..7559bc94b 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -229,7 +229,39 @@ paths:
           content:
             application/json:
               schema:
-                $ref: '#/components/schemas/GetAllExperiments'
+                $ref: '#/components/schemas/ExperimentsList'
+        '400':
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '401':
+          description: The request lacks authentication credentials.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+  '/experiments/examples':
+    get:
+      summary: Get all example experiments
+      description: Get all experiments that are for demonstration
+      operationId: getAllExampleExperiments
+      x-eov-operation-id: experiment#getAllExampleExperiments
+      x-eov-operation-handler: routes/experiment
+      responses:
+        '200':
+          description: All experiments that the user can acess
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ExperimentsList'
         '400':
           description: Bad Request
           content:
@@ -939,6 +971,44 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
+  '/experiments/{experimentId}/clone':
+    post:
+      summary: Clone an experiment
+      description: Clone an experiment, returns the id of the new experiment
+      operationId: cloneExperiment
+      x-eov-operation-id: experiment#clone
+      x-eov-operation-handler: routes/experiment
+      responses:
+        '200':
+          description: Clone experiment
+          content:
+            application/json:
+              schema:
+                type: string
+        '400':
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '401':
+          description: The request lacks authentication credentials.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '403':
+          description: Forbidden request for this user.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
   '/access/{experimentId}':
     get:
       summary: Get the users with access to an experiment
@@ -1460,8 +1530,8 @@ components:
       $ref: './models/experiment-bodies/PatchExperiment.v2.yaml'
     ProcessingConfig:
       $ref: './models/experiment-bodies/ProcessingConfig.v2.yaml'
-    GetAllExperiments:
-      $ref: './models/experiment-bodies/GetAllExperiments.v2.yaml'
+    ExperimentsList:
+      $ref: './models/experiment-bodies/ExperimentsList.v2.yaml'
     CreateSample:
       $ref: './models/samples-bodies/CreateSample.v2.yaml'
     GetSamples:
diff --git a/src/specs/models/experiment-bodies/GetAllExperiments.v2.yaml b/src/specs/models/experiment-bodies/ExperimentsList.v2.yaml
similarity index 100%
rename from src/specs/models/experiment-bodies/GetAllExperiments.v2.yaml
rename to src/specs/models/experiment-bodies/ExperimentsList.v2.yaml

From 73953b610d1f482a818cf590be1e447d1fe4d890 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Tue, 21 Jun 2022 09:21:14 -0300
Subject: [PATCH 02/29] Add return of sample file ids in Sample.getSamples

---
 src/api.v2/model/Sample.js | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/api.v2/model/Sample.js b/src/api.v2/model/Sample.js
index 48a2c5428..47d9bc955 100644
--- a/src/api.v2/model/Sample.js
+++ b/src/api.v2/model/Sample.js
@@ -38,6 +38,11 @@ class Sample extends BasicModel {
     const sampleFileFields = ['sample_file_type', 'size', 'upload_status', 's3_path'];
     const sampleFileFieldsWithAlias = sampleFileFields.map((field) => `sf.${field}`);
     const fileObjectFormatted = sampleFileFields.map((field) => [`'${field}'`, field]);
+
+    // Add sample file id (needs to go separate to avoid conflict with sample id)
+    sampleFileFieldsWithAlias.push('sf.id as sf_id');
+    fileObjectFormatted.push(['\'id\'', 'sf_id']);
+
     const sampleFileObject = `jsonb_object_agg(sample_file_type,json_build_object(${fileObjectFormatted})) as files`;
     const fileNamesQuery = sql.select(['id', sql.raw(sampleFileObject)])
       .from(sql.select([...sampleFileFieldsWithAlias, 's.id'])

From b98719486ea2a2491dc712a279acbad0f290b7c9 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Tue, 21 Jun 2022 15:32:52 -0300
Subject: [PATCH 03/29] Add experiment clone endpoint

---
 .../controllers/experimentController.js       | 26 ++++++--
 src/api.v2/helpers/roles.js                   |  3 +-
 src/api.v2/model/Experiment.js                |  4 +-
 src/api.v2/model/Sample.js                    | 65 +++++++++++++++++++
 src/api.v2/model/UserAccess.js                | 10 ++-
 src/specs/api.v2.yaml                         |  2 +-
 6 files changed, 98 insertions(+), 12 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 6e3791dee..5494b5364 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -8,6 +8,8 @@ const { OK, NotFoundError } = require('../../utils/responses');
 const sqlClient = require('../../sql/sqlClient');
 
 const getExperimentBackendStatus = require('../helpers/backendStatus/getExperimentBackendStatus');
+const Sample = require('../model/Sample');
+const MetadataTrack = require('../model/MetadataTrack');
 
 const logger = getLogger('[ExperimentController] - ');
 
@@ -141,16 +143,28 @@ const downloadData = async (req, res) => {
 };
 
 const cloneExperiment = async (req, res) => {
-  const { experimentId } = req.params;
+  const {
+    params: { experimentId: fromExperimentId, toExperimentId },
+  } = req;
+
+  logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
 
-  logger.log(`Cloning experiment ${experimentId}`);
+  // toExperiment might have metadata tracks,
+  // we want to start from an empty one so clear them out
+  await new MetadataTrack().delete({ experiment_id: toExperimentId });
 
-  const cloneExperimentId = await new Experiment().createClone(experimentId);
-  // const downloadLink = await new SampleFile().getDownloadLink(experimentId, downloadType);
+  const { samplesOrder } = await new Experiment().findById(fromExperimentId).first();
 
-  logger.log(`Finished cloning experiment ${experimentId}, new expeirment's id is ${cloneExperimentId}`);
+  const newSampleIds = await new Sample().copyTo(fromExperimentId, toExperimentId, samplesOrder);
 
-  res.json(cloneExperimentId);
+  await new Experiment().updateById(
+    toExperimentId,
+    { samples_order: JSON.stringify(newSampleIds) },
+  );
+
+  logger.log(`Finished cloning experiment ${fromExperimentId}, new expeirment's id is ${toExperimentId}`);
+
+  res.json(OK());
 };
 
 module.exports = {
diff --git a/src/api.v2/helpers/roles.js b/src/api.v2/helpers/roles.js
index 084dd2f25..653caadb4 100644
--- a/src/api.v2/helpers/roles.js
+++ b/src/api.v2/helpers/roles.js
@@ -18,9 +18,10 @@ const allowedResources = {
     'socket',
     '/experiments/(?<experimentId>.*)/plots-tables/(?<plotUuid>.*)',
     '/experiments/(?<experimentId>.*)/cellSets',
+    '/experiments/(?<experimentId>.*)/clone/.*',
   ],
   [VIEWER]: [
-    '/experiments/(?<experimentId>.*)/clone',
+    '/experiments/(?<experimentId>.*)/clone/.*',
   ],
 };
 const isRoleAuthorized = (role, resource, method) => {
diff --git a/src/api.v2/model/Experiment.js b/src/api.v2/model/Experiment.js
index 107a93626..3ea4cfed3 100644
--- a/src/api.v2/model/Experiment.js
+++ b/src/api.v2/model/Experiment.js
@@ -60,8 +60,8 @@ class Experiment extends BasicModel {
   }
 
   async getAllExampleExperiments() {
-    const noOwnerExperiments = '00000000-0000-0000-0000-000000000000';
-    return this.getAllExperiments(noOwnerExperiments);
+    const publicAccessId = '00000000-0000-0000-0000-000000000000';
+    return this.getAllExperiments(publicAccessId);
   }
 
   async getExperimentData(experimentId) {
diff --git a/src/api.v2/model/Sample.js b/src/api.v2/model/Sample.js
index 47d9bc955..dec7d534f 100644
--- a/src/api.v2/model/Sample.js
+++ b/src/api.v2/model/Sample.js
@@ -1,3 +1,7 @@
+const _ = require('lodash');
+
+const { v4: uuidv4 } = require('uuid');
+
 const BasicModel = require('./BasicModel');
 const sqlClient = require('../../sql/sqlClient');
 
@@ -86,6 +90,67 @@ class Sample extends BasicModel {
       );
     });
   }
+
+  /**
+   * Creates copy samples from one experiment to another one
+   *
+   * @param {*} fromExperimentId
+   * @param {*} toExperimentId
+   */
+  async copyTo(fromExperimentId, toExperimentId, samplesOrder) {
+    const result = await this.getSamples(fromExperimentId);
+
+    const newSampleIds = [];
+
+    const metadataTrackKeys = Object.keys(result[0].metadata);
+
+    const sampleRows = [];
+    const sampleFileMapRows = [];
+    const metadataValueMapRows = [];
+
+    await this.sql.transaction(async (trx) => {
+      const metadataTracks = await trx(tableNames.METADATA_TRACK)
+        .insert(metadataTrackKeys.map((key) => ({ experiment_id: toExperimentId, key })))
+        .returning(['id', 'key']);
+
+      // Copy each sample in order so
+      // the new samples we create follow the same order
+      samplesOrder.forEach((fromSampleId) => {
+        const sample = result.find(({ id }) => id === fromSampleId);
+
+        const toSampleId = uuidv4();
+
+        newSampleIds.push(toSampleId);
+
+        sampleRows.push({
+          id: toSampleId,
+          experiment_id: toExperimentId,
+          name: sample.name,
+          sample_technology: sample.sampleTechnology,
+        });
+
+        Object.entries(sample.files).forEach(([, file]) => {
+          sampleFileMapRows.push({
+            sample_id: toSampleId,
+            sample_file_id: file.id,
+          });
+        });
+
+        Object.entries(sample.metadata).forEach(([key, value]) => {
+          console.log('valueDebug');
+          console.log(value);
+          const { id } = _.find(metadataTracks, ({ key: currentKey }) => currentKey === key);
+          metadataValueMapRows.push({ metadata_track_id: id, sample_id: toSampleId, value });
+        });
+      });
+
+      await trx(tableNames.SAMPLE).insert(sampleRows);
+      await trx(tableNames.SAMPLE_IN_METADATA_TRACK_MAP).insert(metadataValueMapRows);
+      await trx(tableNames.SAMPLE_TO_SAMPLE_FILE_MAP).insert(sampleFileMapRows);
+    });
+
+    return newSampleIds;
+  }
 }
 
 module.exports = Sample;
diff --git a/src/api.v2/model/UserAccess.js b/src/api.v2/model/UserAccess.js
index 26b977b2b..e7d866f79 100644
--- a/src/api.v2/model/UserAccess.js
+++ b/src/api.v2/model/UserAccess.js
@@ -91,11 +91,17 @@ class UserAccess extends BasicModel {
     await this.grantAccess(userId, experimentId, AccessRole.OWNER);
   }
 
+
   async canAccessExperiment(userId, experimentId, url, method) {
+    const publicAccessId = '00000000-0000-0000-0000-000000000000';
+
     const result = await this.sql(tableNames.USER_ACCESS)
-      .first()
+      // Check if user has access
       .where({ experiment_id: experimentId, user_id: userId })
-      .from(tableNames.USER_ACCESS);
+      // Or if it is a public access experiment
+      .orWhere({ experiment_id: experimentId, user_id: publicAccessId })
+      .from(tableNames.USER_ACCESS)
+      .first();
 
     // If there is no entry for this user and role, then user definitely doesn't have access
     if (_.isNil(result)) {
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index 7559bc94b..7e6081686 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -971,7 +971,7 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
-  '/experiments/{experimentId}/clone':
+  '/experiments/{experimentId}/clone/{toExperimentId}':
     post:
       summary: Clone an experiment
       description: Clone an experiment, returns the id of the new experiment

From ffb177a4c8aaac9e51db5339325226e9538ab171 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Tue, 21 Jun 2022 15:49:53 -0300
Subject: [PATCH 04/29] Cleanup

---
 src/api.v2/helpers/worker/getWorkResults.js | 1 -
 src/api.v2/model/Sample.js                  | 2 --
 src/specs/api.v2.yaml                       | 2 +-
 3 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/api.v2/helpers/worker/getWorkResults.js b/src/api.v2/helpers/worker/getWorkResults.js
index 0c1da07f5..20b7e3721 100644
--- a/src/api.v2/helpers/worker/getWorkResults.js
+++ b/src/api.v2/helpers/worker/getWorkResults.js
@@ -52,7 +52,6 @@ const getWorkResults = async (experimentId, ETag) => {
   const formattedExperimentId = formatExperimentId(experimentId);
 
   await validateTagMatching(formattedExperimentId, params);
-  console.log('GETTING WORK RESULTS IWTH PARAMS ', params);
   logger.log(`Found worker results for experiment: ${experimentId}, Etag: ${ETag}`);
 
   const signedUrl = getSignedUrl('getObject', params);
diff --git a/src/api.v2/model/Sample.js b/src/api.v2/model/Sample.js
index dec7d534f..fb79303a9 100644
--- a/src/api.v2/model/Sample.js
+++ b/src/api.v2/model/Sample.js
@@ -137,8 +137,6 @@ class Sample extends BasicModel {
         });
 
         Object.entries(sample.metadata).forEach(([key, value]) => {
-          console.log('valueDebug');
-          console.log(value);
           const { id } = _.find(metadataTracks, ({ key: currentKey }) => currentKey === key);
           metadataValueMapRows.push({ metadata_track_id: id, sample_id: toSampleId, value });
         });
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index 7e6081686..438c1e63c 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -984,7 +984,7 @@ paths:
           content:
             application/json:
               schema:
-                type: string
+                $ref: '#/components/schemas/HTTPSuccess'
         '400':
           description: Bad Request
           content:

From f61c436618317d0af166c85f3f40e7954983cc46 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 09:48:43 -0300
Subject: [PATCH 05/29] Minor readbilitity improvement

---
 src/api.v2/controllers/experimentController.js | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 5494b5364..09a814077 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -153,13 +153,15 @@ const cloneExperiment = async (req, res) => {
   // we want to start from an empty one so clear them out
   await new MetadataTrack().delete({ experiment_id: toExperimentId });
 
+  // Get samples order so we preserve the relative order of the original samples in the cloned ones
   const { samplesOrder } = await new Experiment().findById(fromExperimentId).first();
 
-  const newSampleIds = await new Sample().copyTo(fromExperimentId, toExperimentId, samplesOrder);
+  const cloneSamplesOrder = await new Sample()
+    .copyTo(fromExperimentId, toExperimentId, samplesOrder);
 
   await new Experiment().updateById(
     toExperimentId,
-    { samples_order: JSON.stringify(newSampleIds) },
+    { samples_order: JSON.stringify(cloneSamplesOrder) },
   );
 
   logger.log(`Finished cloning experiment ${fromExperimentId}, new expeirment's id is ${toExperimentId}`);

From 79f7c3fbac7649c737c5afa4856fbbad16d9ab65 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 12:03:58 -0300
Subject: [PATCH 06/29] Update snapshots

---
 tests/api.v2/model/__snapshots__/Sample.test.js.snap | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/api.v2/model/__snapshots__/Sample.test.js.snap b/tests/api.v2/model/__snapshots__/Sample.test.js.snap
index 848e3a747..53141e68e 100644
--- a/tests/api.v2/model/__snapshots__/Sample.test.js.snap
+++ b/tests/api.v2/model/__snapshots__/Sample.test.js.snap
@@ -74,6 +74,7 @@ Array [
       "sf.size",
       "sf.upload_status",
       "sf.s3_path",
+      "sf.id as sf_id",
       "s.id",
     ],
   ],
@@ -127,7 +128,7 @@ Array [
     "undefined as metadata",
   ],
   Array [
-    "jsonb_object_agg(sample_file_type,json_build_object('sample_file_type',sample_file_type,'size',size,'upload_status',upload_status,'s3_path',s3_path)) as files",
+    "jsonb_object_agg(sample_file_type,json_build_object('sample_file_type',sample_file_type,'size',size,'upload_status',upload_status,'s3_path',s3_path,'id',sf_id)) as files",
   ],
 ]
 `;

From 010d4a1c3af497c1f94f4d445451f85e34b3299d Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 13:17:28 -0300
Subject: [PATCH 07/29] Fix tests and minor refactoreing

---
 src/api.v2/model/Experiment.js         |  4 ++--
 src/api.v2/model/UserAccess.js         |  5 ++---
 src/utils/constants.js                 |  3 +++
 tests/api.v2/mocks/getMockSqlClient.js |  1 +
 tests/api.v2/model/UserAccess.test.js  | 20 +++++++++++++++-----
 5 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/src/api.v2/model/Experiment.js b/src/api.v2/model/Experiment.js
index 3ea4cfed3..c6f7dc339 100644
--- a/src/api.v2/model/Experiment.js
+++ b/src/api.v2/model/Experiment.js
@@ -12,6 +12,7 @@ const config = require('../../config');
 const getLogger = require('../../utils/getLogger');
 const bucketNames = require('../helpers/s3/bucketNames');
 const { getSignedUrl } = require('../../utils/aws/s3');
+const constants = require('../../utils/constants');
 
 const logger = getLogger('[ExperimentModel] - ');
 
@@ -60,8 +61,7 @@ class Experiment extends BasicModel {
   }
 
   async getAllExampleExperiments() {
-    const publicAccessId = '00000000-0000-0000-0000-000000000000';
-    return this.getAllExperiments(publicAccessId);
+    return this.getAllExperiments(constants.PUBLIC_ACCESS_ID);
   }
 
   async getExperimentData(experimentId) {
diff --git a/src/api.v2/model/UserAccess.js b/src/api.v2/model/UserAccess.js
index e7d866f79..7c04cc586 100644
--- a/src/api.v2/model/UserAccess.js
+++ b/src/api.v2/model/UserAccess.js
@@ -19,6 +19,7 @@ const selectableProps = [
 ];
 
 const getLogger = require('../../utils/getLogger');
+const constants = require('../../utils/constants');
 
 const logger = getLogger('[UserAccessModel] - ');
 
@@ -93,13 +94,11 @@ class UserAccess extends BasicModel {
 
 
   async canAccessExperiment(userId, experimentId, url, method) {
-    const publicAccessId = '00000000-0000-0000-0000-000000000000';
-
     const result = await this.sql(tableNames.USER_ACCESS)
       // Check if user has access
       .where({ experiment_id: experimentId, user_id: userId })
       // Or if it is a public access experiment
-      .orWhere({ experiment_id: experimentId, user_id: publicAccessId })
+      .orWhere({ experiment_id: experimentId, user_id: constants.PUBLIC_ACCESS_ID })
       .from(tableNames.USER_ACCESS)
       .first();
 
diff --git a/src/utils/constants.js b/src/utils/constants.js
index 62032e0c4..681852d9b 100644
--- a/src/utils/constants.js
+++ b/src/utils/constants.js
@@ -23,6 +23,8 @@ const NOT_CREATED = 'NOT_CREATED';
 const EXECUTION_DOES_NOT_EXIST = 'ExecutionDoesNotExist';
 const ACCESS_DENIED = 'AccessDeniedException';
 
+const PUBLIC_ACCESS_ID = '00000000-0000-0000-0000-000000000000';
+
 module.exports = {
   QC_PROCESS_NAME,
   GEM2S_PROCESS_NAME,
@@ -36,4 +38,5 @@ module.exports = {
   EXECUTION_DOES_NOT_EXIST,
   ACCESS_DENIED,
   ASSIGN_POD_TO_PIPELINE,
+  PUBLIC_ACCESS_ID,
 };
diff --git a/tests/api.v2/mocks/getMockSqlClient.js b/tests/api.v2/mocks/getMockSqlClient.js
index 7251b08e3..5f84c904d 100644
--- a/tests/api.v2/mocks/getMockSqlClient.js
+++ b/tests/api.v2/mocks/getMockSqlClient.js
@@ -20,6 +20,7 @@ module.exports = () => {
     into: jest.fn().mockReturnThis(),
     timeout: jest.fn().mockReturnThis(),
     andWhere: jest.fn().mockReturnThis(),
+    orWhere: jest.fn().mockReturnThis(),
     whereExists: jest.fn().mockReturnThis(),
     whereIn: jest.fn().mockReturnThis(),
     queryContext: jest.fn().mockReturnThis(),
diff --git a/tests/api.v2/model/UserAccess.test.js b/tests/api.v2/model/UserAccess.test.js
index 5c4d9d213..c80d046db 100644
--- a/tests/api.v2/model/UserAccess.test.js
+++ b/tests/api.v2/model/UserAccess.test.js
@@ -22,6 +22,7 @@ jest.mock('../../../src/utils/aws/user', () => ({
 const BasicModel = require('../../../src/api.v2/model/BasicModel');
 const UserAccess = require('../../../src/api.v2/model/UserAccess');
 const AccessRole = require('../../../src/utils/enums/AccessRole');
+const constants = require('../../../src/utils/constants');
 
 const mockAdminUserId = testConfig.adminSub;
 const mockUserId = '1234-5678-9012-1234';
@@ -200,18 +201,21 @@ describe('model/userAccess', () => {
     const url = 'url';
     const method = 'method';
 
-    mockSqlClient.from.mockImplementationOnce(() => ({ accessRole: 'roleThatIsOk' }));
+    mockSqlClient.first.mockImplementationOnce(() => ({ accessRole: 'roleThatIsOk' }));
 
     roles.isRoleAuthorized.mockImplementationOnce(() => true);
 
-    const result = await new UserAccess().canAccessExperiment(mockUserId, mockExperimentId, url, method);
-
+    const result = await new UserAccess()
+      .canAccessExperiment(mockUserId, mockExperimentId, url, method);
 
     expect(mockSqlClient.first).toHaveBeenCalled();
     expect(mockSqlClient.from).toHaveBeenCalledWith('user_access');
     expect(mockSqlClient.where).toHaveBeenCalledWith(
       { experiment_id: mockExperimentId, user_id: mockUserId },
     );
+    expect(mockSqlClient.orWhere).toHaveBeenCalledWith(
+      { experiment_id: mockExperimentId, user_id: constants.PUBLIC_ACCESS_ID },
+    );
 
     expect(roles.isRoleAuthorized).toHaveBeenCalledWith('roleThatIsOk', url, method);
     expect(result).toEqual(true);
@@ -221,7 +225,7 @@ describe('model/userAccess', () => {
     const url = 'url';
     const method = 'method';
 
-    mockSqlClient.from.mockImplementationOnce(() => undefined);
+    mockSqlClient.first.mockImplementationOnce(() => undefined);
 
     const result = await new UserAccess().canAccessExperiment(mockUserId, mockExperimentId, url, method);
 
@@ -230,6 +234,9 @@ describe('model/userAccess', () => {
     expect(mockSqlClient.where).toHaveBeenCalledWith(
       { experiment_id: mockExperimentId, user_id: mockUserId },
     );
+    expect(mockSqlClient.orWhere).toHaveBeenCalledWith(
+      { experiment_id: mockExperimentId, user_id: constants.PUBLIC_ACCESS_ID },
+    );
 
     expect(roles.isRoleAuthorized).not.toHaveBeenCalled();
 
@@ -240,7 +247,7 @@ describe('model/userAccess', () => {
     const url = 'url';
     const method = 'method';
 
-    mockSqlClient.from.mockImplementationOnce(() => ({ accessRole: 'roleThatIsNotOk' }));
+    mockSqlClient.first.mockImplementationOnce(() => ({ accessRole: 'roleThatIsNotOk' }));
 
     roles.isRoleAuthorized.mockImplementationOnce(() => false);
 
@@ -251,6 +258,9 @@ describe('model/userAccess', () => {
     expect(mockSqlClient.where).toHaveBeenCalledWith(
       { experiment_id: mockExperimentId, user_id: mockUserId },
     );
+    expect(mockSqlClient.orWhere).toHaveBeenCalledWith(
+      { experiment_id: mockExperimentId, user_id: constants.PUBLIC_ACCESS_ID },
+    );
 
     expect(roles.isRoleAuthorized).toHaveBeenCalledWith('roleThatIsNotOk', url, method);
 

From 6c573c483e4f4d4774e8557d6bc3b91302c488f2 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 13:22:13 -0300
Subject: [PATCH 08/29] Update model/experiment tests

---
 tests/api.v2/model/Experiment.test.js         | 15 +-------------
 .../__snapshots__/Experiment.test.js.snap     | 20 +++++++++++++++++++
 2 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/tests/api.v2/model/Experiment.test.js b/tests/api.v2/model/Experiment.test.js
index d1abfea52..3dfaee51b 100644
--- a/tests/api.v2/model/Experiment.test.js
+++ b/tests/api.v2/model/Experiment.test.js
@@ -47,20 +47,7 @@ describe('model/Experiment', () => {
     expect(queryResult).toEqual(expectedResult);
 
     expect(sqlClient.get).toHaveBeenCalled();
-    expect(helpers.collapseKeyIntoArray).toHaveBeenCalledWith(
-      expect.any(Function),
-      ['id', 'name', 'description', 'samples_order', 'notify_by_email', 'created_at', 'updated_at'],
-      'key',
-      'metadataKeys',
-      mockSqlClient,
-    );
-
-
-    // Check that mainQuery is correct
-    const mainQuery = helpers.collapseKeyIntoArray.mock.calls[0][0];
-
-    jest.clearAllMocks();
-    await mainQuery.bind(mockSqlClient)();
+    expect(helpers.collapseKeyIntoArray.mock.calls).toMatchSnapshot();
 
     expect(mockSqlClient.select).toHaveBeenCalledWith(
       ['e.id', 'e.name', 'e.description', 'e.samples_order', 'e.notify_by_email', 'e.created_at', 'e.updated_at', 'm.key'],
diff --git a/tests/api.v2/model/__snapshots__/Experiment.test.js.snap b/tests/api.v2/model/__snapshots__/Experiment.test.js.snap
index 60e0c5761..078a132db 100644
--- a/tests/api.v2/model/__snapshots__/Experiment.test.js.snap
+++ b/tests/api.v2/model/__snapshots__/Experiment.test.js.snap
@@ -1,5 +1,25 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
+exports[`model/Experiment getAllExperiments works correctly 1`] = `
+Array [
+  Array [
+    [MockFunction],
+    Array [
+      "id",
+      "name",
+      "description",
+      "samples_order",
+      "notify_by_email",
+      "created_at",
+      "updated_at",
+    ],
+    "key",
+    "metadataKeys",
+    [MockFunction],
+  ],
+]
+`;
+
 exports[`model/Experiment getExperimentData works correctly 1`] = `
 Array [
   "COALESCE(

From 3934bd75388322702fb2d1b86b2378f08c9675ff Mon Sep 17 00:00:00 2001
From: Martin Fosco <cosa65@users.noreply.github.com>
Date: Wed, 22 Jun 2022 13:50:33 -0300
Subject: [PATCH 09/29] Update experimentController.js

---
 src/api.v2/controllers/experimentController.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 09a814077..4b8071cbb 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -149,8 +149,8 @@ const cloneExperiment = async (req, res) => {
 
   logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
 
-  // toExperiment might have metadata tracks,
-  // we want to start from an empty one so clear them out
+  // toExperiment might have pre existing metadata tracks,
+  // we want to start without any old ones so we clear them out
   await new MetadataTrack().delete({ experiment_id: toExperimentId });
 
   // Get samples order so we preserve the relative order of the original samples in the cloned ones

From fb5da33fa36950f2387600b10404ee7aa216010f Mon Sep 17 00:00:00 2001
From: Martin Fosco <cosa65@users.noreply.github.com>
Date: Wed, 22 Jun 2022 13:56:54 -0300
Subject: [PATCH 10/29] Update experimentController.js

---
 src/api.v2/controllers/experimentController.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 4b8071cbb..2d46d342f 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -149,8 +149,8 @@ const cloneExperiment = async (req, res) => {
 
   logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
 
-  // toExperiment might have pre existing metadata tracks,
-  // we want to start without any old ones so we clear them out
+  // toExperiment might be an old experiment with metadata tracks,
+  // we want to start without any old tracks so clear them out
   await new MetadataTrack().delete({ experiment_id: toExperimentId });
 
   // Get samples order so we preserve the relative order of the original samples in the cloned ones

From d02bd4de70557c4f14ba61ef66c08b88fad55769 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 14:14:30 -0300
Subject: [PATCH 11/29] Add samplesSubsetIds optional body in clone endpoint

---
 src/api.v2/controllers/experimentController.js | 12 +++++++++---
 src/specs/api.v2.yaml                          | 12 ++++++++++++
 tests/api.v2/model/Sample.test.js              |  1 +
 3 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 2d46d342f..611e5306b 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -145,6 +145,7 @@ const downloadData = async (req, res) => {
 const cloneExperiment = async (req, res) => {
   const {
     params: { experimentId: fromExperimentId, toExperimentId },
+    body: { samplesSubsetIds = null },
   } = req;
 
   logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
@@ -153,11 +154,16 @@ const cloneExperiment = async (req, res) => {
   // we want to start without any old tracks so clear them out
   await new MetadataTrack().delete({ experiment_id: toExperimentId });
 
-  // Get samples order so we preserve the relative order of the original samples in the cloned ones
-  const { samplesOrder } = await new Experiment().findById(fromExperimentId).first();
+  let samplesToCloneIds = samplesSubsetIds;
+  if (!samplesToCloneIds) {
+    // Get samples order so we preserve
+    // the relative order of the original samples in the cloned ones
+    const { samplesOrder } = await new Experiment().findById(fromExperimentId).first();
+    samplesToCloneIds = samplesOrder;
+  }
 
   const cloneSamplesOrder = await new Sample()
-    .copyTo(fromExperimentId, toExperimentId, samplesOrder);
+    .copyTo(fromExperimentId, toExperimentId, samplesToCloneIds);
 
   await new Experiment().updateById(
     toExperimentId,
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index ea910b6db..47e1c8105 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -1193,6 +1193,18 @@ paths:
       operationId: cloneExperiment
       x-eov-operation-id: experiment#clone
       x-eov-operation-handler: routes/experiment
+      requestBody:
+        content:
+          application/json:
+            schema:
+              description: If samplesSubsetIds is sent then the cloned experiment only contains the subset samples instead of all of them
+              type: object
+              properties:
+                samplesSubsetIds:
+                  type: array
+                  items:
+                    type: string   
+              additionalProperties: false
       responses:
         '200':
           description: Clone experiment
diff --git a/tests/api.v2/model/Sample.test.js b/tests/api.v2/model/Sample.test.js
index 3c9d4e1e8..722db48c9 100644
--- a/tests/api.v2/model/Sample.test.js
+++ b/tests/api.v2/model/Sample.test.js
@@ -1,3 +1,4 @@
+// @ts-nocheck
 const { mockSqlClient, mockTrx } = require('../mocks/getMockSqlClient')();
 
 const Sample = require('../../../src/api.v2/model/Sample');

From 8dd4956aecfb1c08a7e4b5332c84571d4d335c6e Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 14:18:26 -0300
Subject: [PATCH 12/29] Rename

---
 src/api.v2/controllers/experimentController.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 611e5306b..dee7e78f5 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -162,12 +162,12 @@ const cloneExperiment = async (req, res) => {
     samplesToCloneIds = samplesOrder;
   }
 
-  const cloneSamplesOrder = await new Sample()
+  const clonedSamplesOrder = await new Sample()
     .copyTo(fromExperimentId, toExperimentId, samplesToCloneIds);
 
   await new Experiment().updateById(
     toExperimentId,
-    { samples_order: JSON.stringify(cloneSamplesOrder) },
+    { samples_order: JSON.stringify(clonedSamplesOrder) },
   );
 
   logger.log(`Finished cloning experiment ${fromExperimentId}, new expeirment's id is ${toExperimentId}`);

From 9796c2a0d28107500e15432c496c5ceb15681d93 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 14:32:58 -0300
Subject: [PATCH 13/29] Refactor way in which we get the sample ids

---
 src/api.v2/controllers/experimentController.js | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index dee7e78f5..dbb50998b 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -142,10 +142,16 @@ const downloadData = async (req, res) => {
   res.json(downloadLink);
 };
 
+
 const cloneExperiment = async (req, res) => {
+  const getAllSampleIds = async (experimentId) => {
+    const { samplesOrder } = await new Experiment().findById(experimentId).first();
+    return samplesOrder;
+  };
+
   const {
     params: { experimentId: fromExperimentId, toExperimentId },
-    body: { samplesSubsetIds = null },
+    body: { samplesSubsetIds = await getAllSampleIds(fromExperimentId) },
   } = req;
 
   logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
@@ -154,16 +160,8 @@ const cloneExperiment = async (req, res) => {
   // we want to start without any old tracks so clear them out
   await new MetadataTrack().delete({ experiment_id: toExperimentId });
 
-  let samplesToCloneIds = samplesSubsetIds;
-  if (!samplesToCloneIds) {
-    // Get samples order so we preserve
-    // the relative order of the original samples in the cloned ones
-    const { samplesOrder } = await new Experiment().findById(fromExperimentId).first();
-    samplesToCloneIds = samplesOrder;
-  }
-
   const clonedSamplesOrder = await new Sample()
-    .copyTo(fromExperimentId, toExperimentId, samplesToCloneIds);
+    .copyTo(fromExperimentId, toExperimentId, samplesSubsetIds);
 
   await new Experiment().updateById(
     toExperimentId,

From 5d3390d0ff34c0eb426e532c1f144f53bfd406d5 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 14:53:38 -0300
Subject: [PATCH 14/29] Add model/Sample copyTo tests

---
 .../api.v2/mocks/data/getSamplesResponse.json | 70 ++++++++++++++++
 tests/api.v2/model/Sample.test.js             | 27 ++++++
 .../model/__snapshots__/Sample.test.js.snap   | 82 +++++++++++++++++++
 3 files changed, 179 insertions(+)
 create mode 100644 tests/api.v2/mocks/data/getSamplesResponse.json

diff --git a/tests/api.v2/mocks/data/getSamplesResponse.json b/tests/api.v2/mocks/data/getSamplesResponse.json
new file mode 100644
index 000000000..3d2aeaddf
--- /dev/null
+++ b/tests/api.v2/mocks/data/getSamplesResponse.json
@@ -0,0 +1,70 @@
+[
+  {
+      "id": "4058acff-3dd4-4a0b-9bff-bb4c1b9a69e5",
+      "experimentId": "d3031abeeac4aaf94f05a9b543779e09",
+      "name": "KO",
+      "sampleTechnology": "10x",
+      "createdAt": "2022-06-22 17:35:40.427554+00",
+      "updatedAt": "2022-06-22 17:35:40.427554+00",
+      "metadata": {
+          "Track0": "N.A.1"
+      },
+      "files": {
+          "matrix10x": {
+              "id": "2afe253f-5542-4a90-9fc9-17acdc3ecaf1",
+              "size": 25581681,
+              "s3Path": "2afe253f-5542-4a90-9fc9-17acdc3ecaf1",
+              "uploadStatus": "uploaded",
+              "sampleFileType": "matrix10x"
+          },
+          "barcodes10x": {
+              "id": "59b8221d-dd3f-4bb9-ad9d-1166471e7143",
+              "size": 21715,
+              "s3Path": "59b8221d-dd3f-4bb9-ad9d-1166471e7143",
+              "uploadStatus": "uploaded",
+              "sampleFileType": "barcodes10x"
+          },
+          "features10x": {
+              "id": "415323cb-72dc-4f42-b452-c12422ea042f",
+              "size": 279361,
+              "s3Path": "415323cb-72dc-4f42-b452-c12422ea042f",
+              "uploadStatus": "uploaded",
+              "sampleFileType": "features10x"
+          }
+      }
+  },
+  {
+      "id": "908b7d7a-e1fe-4285-82b0-47c4cf7cc2bf",
+      "experimentId": "d3031abeeac4aaf94f05a9b543779e09",
+      "name": "WT1",
+      "sampleTechnology": "10x",
+      "createdAt": "2022-06-22 17:44:02.155432+00",
+      "updatedAt": "2022-06-22 17:44:02.155432+00",
+      "metadata": {
+          "Track0": "N.A."
+      },
+      "files": {
+          "matrix10x": {
+              "id": "d5c957b9-a6cb-4828-8ee6-1f9da8cacb6a",
+              "size": 5079737,
+              "s3Path": "d5c957b9-a6cb-4828-8ee6-1f9da8cacb6a",
+              "uploadStatus": "uploaded",
+              "sampleFileType": "matrix10x"
+          },
+          "barcodes10x": {
+              "id": "d52a84a8-4669-41b3-a8d1-38e16ddbf522",
+              "size": 5331,
+              "s3Path": "d52a84a8-4669-41b3-a8d1-38e16ddbf522",
+              "uploadStatus": "uploaded",
+              "sampleFileType": "barcodes10x"
+          },
+          "features10x": {
+              "id": "5b8ec36c-0f06-4a65-b924-da5189c89b7b",
+              "size": 279361,
+              "s3Path": "5b8ec36c-0f06-4a65-b924-da5189c89b7b",
+              "uploadStatus": "uploaded",
+              "sampleFileType": "features10x"
+          }
+      }
+  }
+]
\ No newline at end of file
diff --git a/tests/api.v2/model/Sample.test.js b/tests/api.v2/model/Sample.test.js
index 722db48c9..c351a74b3 100644
--- a/tests/api.v2/model/Sample.test.js
+++ b/tests/api.v2/model/Sample.test.js
@@ -3,6 +3,8 @@ const { mockSqlClient, mockTrx } = require('../mocks/getMockSqlClient')();
 
 const Sample = require('../../../src/api.v2/model/Sample');
 
+const getSamplesResponse = require('../mocks/data/getSamplesResponse.json');
+
 const mockExperimentId = 'mockExperimentId';
 // @ts-nocheck
 // Disabled ts because it doesn't recognize jest mocks
@@ -65,4 +67,29 @@ describe('model/Sample', () => {
       sample_file_id: mockSampleFileId,
     });
   });
+
+  it('copyTo works correctly if valid params are passed', async () => {
+    const fromExperimentId = 'fromExperimentIdMock';
+    const toExperimentId = 'toExperimentIdMock';
+    const samplesOrder = Object.values(getSamplesResponse).map((sample) => sample.id);
+
+    mockTrx.returning.mockImplementationOnce(() => Promise.resolve([{ id: 0, key: 'Track0' }]));
+
+    const getSamplesSpy = jest.spyOn(Sample.prototype, 'getSamples')
+      .mockImplementationOnce(() => Promise.resolve(getSamplesResponse));
+
+
+    await new Sample().copyTo(fromExperimentId, toExperimentId, samplesOrder);
+
+
+    expect(getSamplesSpy).toHaveBeenCalledWith(fromExperimentId);
+
+    expect(mockTrx).toHaveBeenCalledWith(tableNames.METADATA_TRACK);
+    expect(mockTrx).toHaveBeenCalledWith(tableNames.SAMPLE);
+    expect(mockTrx).toHaveBeenCalledWith(tableNames.SAMPLE_IN_METADATA_TRACK_MAP);
+    expect(mockTrx).toHaveBeenCalledWith(tableNames.SAMPLE_TO_SAMPLE_FILE_MAP);
+
+    expect(mockTrx.insert.mock.calls).toMatchSnapshot();
+    expect(mockTrx.returning.mock.calls).toMatchSnapshot();
+  });
 });
diff --git a/tests/api.v2/model/__snapshots__/Sample.test.js.snap b/tests/api.v2/model/__snapshots__/Sample.test.js.snap
index 53141e68e..e435474a2 100644
--- a/tests/api.v2/model/__snapshots__/Sample.test.js.snap
+++ b/tests/api.v2/model/__snapshots__/Sample.test.js.snap
@@ -149,3 +149,85 @@ Array [
   ],
 ]
 `;
+
+exports[`model/Sample copyTo works correctly if valid params are passed 1`] = `
+Array [
+  Array [
+    Array [
+      Object {
+        "experiment_id": "toExperimentIdMock",
+        "key": "Track0",
+      },
+    ],
+  ],
+  Array [
+    Array [
+      Object {
+        "experiment_id": "toExperimentIdMock",
+        "id": "mock-uuid",
+        "name": "KO",
+        "sample_technology": "10x",
+      },
+      Object {
+        "experiment_id": "toExperimentIdMock",
+        "id": "mock-uuid",
+        "name": "WT1",
+        "sample_technology": "10x",
+      },
+    ],
+  ],
+  Array [
+    Array [
+      Object {
+        "metadata_track_id": 0,
+        "sample_id": "mock-uuid",
+        "value": "N.A.1",
+      },
+      Object {
+        "metadata_track_id": 0,
+        "sample_id": "mock-uuid",
+        "value": "N.A.",
+      },
+    ],
+  ],
+  Array [
+    Array [
+      Object {
+        "sample_file_id": "2afe253f-5542-4a90-9fc9-17acdc3ecaf1",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "59b8221d-dd3f-4bb9-ad9d-1166471e7143",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "415323cb-72dc-4f42-b452-c12422ea042f",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "d5c957b9-a6cb-4828-8ee6-1f9da8cacb6a",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "d52a84a8-4669-41b3-a8d1-38e16ddbf522",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "5b8ec36c-0f06-4a65-b924-da5189c89b7b",
+        "sample_id": "mock-uuid",
+      },
+    ],
+  ],
+]
+`;
+
+exports[`model/Sample copyTo works correctly if valid params are passed 2`] = `
+Array [
+  Array [
+    Array [
+      "id",
+      "key",
+    ],
+  ],
+]
+`;

From 1c0ca31ded9d72ebab5f60b123f18a7928ca1b10 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 14:57:48 -0300
Subject: [PATCH 15/29] Add getAllExampleExperiments test

---
 tests/api.v2/model/Experiment.test.js | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/api.v2/model/Experiment.test.js b/tests/api.v2/model/Experiment.test.js
index 3dfaee51b..1a0722b04 100644
--- a/tests/api.v2/model/Experiment.test.js
+++ b/tests/api.v2/model/Experiment.test.js
@@ -27,6 +27,7 @@ jest.mock('../../../src/sql/helpers', () => ({
 }));
 
 const Experiment = require('../../../src/api.v2/model/Experiment');
+const constants = require('../../../src/utils/constants');
 
 const mockExperimentId = 'mockExperimentId';
 const mockSampleId = 'mockSampleId';
@@ -59,6 +60,18 @@ describe('model/Experiment', () => {
     expect(mockSqlClient.as).toHaveBeenCalledWith('mainQuery');
   });
 
+  it('getAllExampleExperiments works correctly', async () => {
+    const expectedResult = { isMockResult: true };
+
+    const getAllExperimentsSpy = jest.spyOn(Experiment.prototype, 'getAllExperiments')
+      .mockImplementationOnce(() => Promise.resolve(expectedResult));
+
+    const result = await new Experiment().getAllExampleExperiments('mockUserId');
+
+    expect(result).toBe(expectedResult);
+    expect(getAllExperimentsSpy).toHaveBeenCalledWith(constants.PUBLIC_ACCESS_ID);
+  });
+
   it('getExperimentData works correctly', async () => {
     const experimentFields = [
       'id', 'name', 'description',

From 0985cbb33b0034e385cbbfccfbc12e83325bba62 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 15:06:52 -0300
Subject: [PATCH 16/29] Add route tests

---
 tests/api.v2/routes/experiment.test.js | 95 ++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)

diff --git a/tests/api.v2/routes/experiment.test.js b/tests/api.v2/routes/experiment.test.js
index b4d08c828..0f7cb4629 100644
--- a/tests/api.v2/routes/experiment.test.js
+++ b/tests/api.v2/routes/experiment.test.js
@@ -1,6 +1,7 @@
 // @ts-nocheck
 const express = require('express');
 const request = require('supertest');
+const { send } = require('process');
 const expressLoader = require('../../../src/loaders/express');
 
 const { OK } = require('../../../src/utils/responses');
@@ -21,6 +22,8 @@ jest.mock('../../../src/api.v2/controllers/experimentController', () => ({
   getProcessingConfig: jest.fn(),
   updateProcessingConfig: jest.fn(),
   downloadData: jest.fn(),
+  getAllExampleExperiments: jest.fn(),
+  cloneExperiment: jest.fn(),
 }));
 
 jest.mock('../../../src/api.v2/middlewares/authMiddlewares');
@@ -312,4 +315,96 @@ describe('tests for experiment route', () => {
         return done();
       });
   });
+
+  it('getAllExampleExperiments results in a successful response', async (done) => {
+    experimentController.getAllExampleExperiments.mockImplementationOnce((req, res) => {
+      res.json(getExperimentResponse);
+      return Promise.resolve();
+    });
+
+    request(app)
+      .get('/v2/experiments/examples')
+      .expect(200)
+      .end((err) => {
+        if (err) {
+          return done(err);
+        }
+        // there is no point testing for the values of the response body
+        // - if something is wrong, the schema validator will catch it
+        return done();
+      });
+  });
+
+  it('cloneExperiment results in a successful response without a body', async (done) => {
+    const experimentId = 'fromExperimentId';
+    const toExperimentId = 'toExperimentId';
+
+    experimentController.cloneExperiment.mockImplementationOnce((req, res) => {
+      res.json(OK());
+      return Promise.resolve();
+    });
+
+    request(app)
+      .post(`/v2/experiments/${experimentId}/clone/${toExperimentId}`)
+      .set({ 'Content-Type': 'application/json' })
+      .expect(200)
+      .end((err) => {
+        if (err) {
+          return done(err);
+        }
+        // there is no point testing for the values of the response body
+        // - if something is wrong, the schema validator will catch it
+        return done();
+      });
+  });
+
+  it('cloneExperiment results in a successful response with a valid body', async (done) => {
+    const experimentId = 'fromExperimentId';
+    const toExperimentId = 'toExperimentId';
+
+    const body = { samplesSubsetIds: ['sampleId1', 'sampleId2'] };
+
+    experimentController.cloneExperiment.mockImplementationOnce((req, res) => {
+      res.json(OK());
+      return Promise.resolve();
+    });
+
+    request(app)
+      .post(`/v2/experiments/${experimentId}/clone/${toExperimentId}`)
+      .send(body)
+      .expect(200)
+      .end((err) => {
+        if (err) {
+          return done(err);
+        }
+        // there is no point testing for the values of the response body
+        // - if something is wrong, the schema validator will catch it
+        return done();
+      });
+  });
+
+  it('cloneExperiment results in a 400 with an invalid body', async (done) => {
+    const experimentId = 'fromExperimentId';
+    const toExperimentId = 'toExperimentId';
+
+    const body = { samplesSubsetIdsInvalid: ['sampleId1', 'sampleId2'] };
+
+    experimentController.cloneExperiment.mockImplementationOnce((req, res) => {
+      res.json(OK());
+      return Promise.resolve();
+    });
+
+    request(app)
+      .post(`/v2/experiments/${experimentId}/clone/${toExperimentId}`)
+      .send(body)
+      .expect(400)
+      .end((err) => {
+        if (err) {
+          return done(err);
+        }
+        // there is no point testing for the values of the response body
+        // - if something is wrong, the schema validator will catch it
+        return done();
+      });
+  });
 });

From 10cd9f7f935026b938cdd544053ea631d4a4083a Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 15:10:04 -0300
Subject: [PATCH 17/29] Add some logs

---
 src/api.v2/controllers/experimentController.js | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index dbb50998b..6a0f83ae7 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -15,34 +15,36 @@ const logger = getLogger('[ExperimentController] - ');
 
 const getAllExperiments = async (req, res) => {
   const { user: { sub: userId } } = req;
+  console.log(`Getting all experiments for user: ${userId}`);
 
   const data = await new Experiment().getAllExperiments(userId);
 
+  console.log(`Finished getting all experiments for user: ${userId}, length: ${data.length}`);
   res.json(data);
 };
 
 const getAllExampleExperiments = async (req, res) => {
+  console.log('Getting example experiments');
+
   const data = await new Experiment().getAllExampleExperiments();
 
+  console.log(`Finished getting example experiments, length: ${data.length}`);
   res.json(data);
 };
 
 const getExperiment = async (req, res) => {
   const { params: { experimentId } } = req;
-
   logger.log(`Getting experiment ${experimentId}`);
 
   const data = await new Experiment().getExperimentData(experimentId);
 
   logger.log(`Finished getting experiment ${experimentId}`);
-
   res.json(data);
 };
 
 const createExperiment = async (req, res) => {
   const { params: { experimentId }, user, body } = req;
   const { name, description } = body;
-
   logger.log('Creating experiment');
 
   await sqlClient.get().transaction(async (trx) => {
@@ -76,7 +78,6 @@ const deleteExperiment = async (req, res) => {
     throw new NotFoundError(`Experiment ${experimentId} not found`);
   }
 
-
   logger.log(`Finished deleting experiment ${experimentId}`);
   res.json(OK());
 };

From dd3157eb16decaa8411da1fcc9bdde29e4b6f5e1 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 15:12:32 -0300
Subject: [PATCH 18/29] Add tests for experimentController

---
 src/api.v2/model/__mocks__/Experiment.js            |  1 +
 src/api.v2/model/__mocks__/Sample.js                |  1 +
 .../api.v2/controllers/experimentController.test.js | 13 +++++++++++++
 3 files changed, 15 insertions(+)

diff --git a/src/api.v2/model/__mocks__/Experiment.js b/src/api.v2/model/__mocks__/Experiment.js
index 0ac3d61e9..2df9fe5aa 100644
--- a/src/api.v2/model/__mocks__/Experiment.js
+++ b/src/api.v2/model/__mocks__/Experiment.js
@@ -9,6 +9,7 @@ const stub = {
   addSample: jest.fn(),
   deleteSample: jest.fn(),
   getDownloadLink: jest.fn(),
+  getAllExampleExperiments: jest.fn(),
   ...BasicModel,
 };
 
diff --git a/src/api.v2/model/__mocks__/Sample.js b/src/api.v2/model/__mocks__/Sample.js
index a8b8e1688..637a79bcd 100644
--- a/src/api.v2/model/__mocks__/Sample.js
+++ b/src/api.v2/model/__mocks__/Sample.js
@@ -3,6 +3,7 @@ const BasicModel = require('./BasicModel')();
 const stub = {
   getSamples: jest.fn(),
   setNewFile: jest.fn(),
+  copyTo: jest.fn(),
   ...BasicModel,
 };
 
diff --git a/tests/api.v2/controllers/experimentController.test.js b/tests/api.v2/controllers/experimentController.test.js
index 0b0feebaa..486181f40 100644
--- a/tests/api.v2/controllers/experimentController.test.js
+++ b/tests/api.v2/controllers/experimentController.test.js
@@ -70,6 +70,19 @@ describe('experimentController', () => {
     expect(mockRes.json).toHaveBeenCalledWith(getAllExperimentsResponse);
   });
 
+  it('getAllExperiments works correctly', async () => {
+    const mockReq = { user: { sub: 'mockUserId' } };
+
+    experimentInstance.getAllExampleExperiments.mockImplementationOnce(
+      () => Promise.resolve(getAllExperimentsResponse),
+    );
+
+    await experimentController.getAllExampleExperiments(mockReq, mockRes);
+
+    expect(experimentInstance.getAllExampleExperiments).toHaveBeenCalled();
+    expect(mockRes.json).toHaveBeenCalledWith(getAllExperimentsResponse);
+  });
+
   it('getExperiment works correctly', async () => {
     const mockReq = { params: { experimentId: getExperimentResponse.id } };
 

From 252bf91656ca5f3d5d45ab856eddd9971a8a405b Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 15:33:25 -0300
Subject: [PATCH 19/29] Add experimentController.cloneExperiment tests

---
 .../controllers/experimentController.test.js  | 76 ++++++++++++++++++-
 1 file changed, 75 insertions(+), 1 deletion(-)

diff --git a/tests/api.v2/controllers/experimentController.test.js b/tests/api.v2/controllers/experimentController.test.js
index 486181f40..674abcef6 100644
--- a/tests/api.v2/controllers/experimentController.test.js
+++ b/tests/api.v2/controllers/experimentController.test.js
@@ -1,6 +1,8 @@
 // @ts-nocheck
 const Experiment = require('../../../src/api.v2/model/Experiment');
+const Sample = require('../../../src/api.v2/model/Sample');
 const UserAccess = require('../../../src/api.v2/model/UserAccess');
+const MetadataTrack = require('../../../src/api.v2/model/MetadataTrack');
 const { mockSqlClient, mockTrx } = require('../mocks/getMockSqlClient')();
 
 const getPipelineStatus = require('../../../src/api.v2/helpers/pipeline/getPipelineStatus');
@@ -9,6 +11,8 @@ const getWorkerStatus = require('../../../src/api.v2/helpers/worker/getWorkerSta
 const bucketNames = require('../../../src/api.v2/helpers/s3/bucketNames');
 
 const experimentInstance = Experiment();
+const sampleTrackInstance = Sample();
+const metadataTrackInstance = MetadataTrack();
 const userAccessInstance = UserAccess();
 
 const mockExperiment = {
@@ -22,7 +26,10 @@ const mockExperiment = {
 };
 
 jest.mock('../../../src/api.v2/model/Experiment');
+jest.mock('../../../src/api.v2/model/Sample');
 jest.mock('../../../src/api.v2/model/UserAccess');
+jest.mock('../../../src/api.v2/model/MetadataTrack');
+
 jest.mock('../../../src/sql/sqlClient', () => ({
   get: jest.fn(() => mockSqlClient),
 }));
@@ -70,7 +77,7 @@ describe('experimentController', () => {
     expect(mockRes.json).toHaveBeenCalledWith(getAllExperimentsResponse);
   });
 
-  it('getAllExperiments works correctly', async () => {
+  it('getAllExampleExperiments works correctly', async () => {
     const mockReq = { user: { sub: 'mockUserId' } };
 
     experimentInstance.getAllExampleExperiments.mockImplementationOnce(
@@ -279,4 +286,71 @@ describe('experimentController', () => {
     expect(experimentInstance.getDownloadLink)
       .toHaveBeenCalledWith(mockExperiment.id, bucketNames.PROCESSED_MATRIX);
   });
+
+  it('cloneExperiment works correctly when samplesSubsetIds is provided', async () => {
+    const toExperimentId = 'toExperimentIdMock';
+    const samplesSubsetIds = ['mockSample2', 'mockSample3'];
+    const clonedSamplesSubsetIds = ['mockClonedSample2', 'mockClonedSample3'];
+
+    const mockReq = {
+      params: { experimentId: mockExperiment.id, toExperimentId },
+      body: { samplesSubsetIds },
+    };
+
+    metadataTrackInstance.delete.mockImplementationOnce(() => Promise.resolve());
+    sampleTrackInstance.copyTo.mockImplementationOnce(
+      () => Promise.resolve(clonedSamplesSubsetIds),
+    );
+    experimentInstance.updateById.mockImplementationOnce(() => Promise.resolve());
+
+    await experimentController.cloneExperiment(mockReq, mockRes);
+
+    expect(metadataTrackInstance.delete).toHaveBeenCalledWith({ experiment_id: toExperimentId });
+
+    expect(sampleTrackInstance.copyTo)
+      .toHaveBeenCalledWith(mockExperiment.id, toExperimentId, samplesSubsetIds);
+
+    expect(experimentInstance.updateById).toHaveBeenCalledWith(
+      toExperimentId,
+      { samples_order: JSON.stringify(clonedSamplesSubsetIds) },
+    );
+
+    expect(mockRes.json).toHaveBeenCalledWith(OK());
+  });
+
+  it('cloneExperiment works correctly when samplesSubsetIds is NOT provided', async () => {
+    const toExperimentId = 'toExperimentIdMock';
+    const allSampleIds = ['mockSample1', 'mockSample2', 'mockSample3', 'mockSample4'];
+    const clonedSamplesIds = ['mockClonedSample1', 'mockClonedSample2', 'mockClonedSample3', 'mockClonedSample4'];
+
+    const mockReq = {
+      params: { experimentId: mockExperiment.id, toExperimentId },
+      body: {},
+    };
+
+    experimentInstance.findById.mockReturnValueOnce(
+      { first: () => Promise.resolve({ samplesOrder: allSampleIds }) },
+    );
+    metadataTrackInstance.delete.mockImplementationOnce(() => Promise.resolve());
+    sampleTrackInstance.copyTo.mockImplementationOnce(
+      () => Promise.resolve(clonedSamplesIds),
+    );
+    experimentInstance.updateById.mockImplementationOnce(() => Promise.resolve());
+
+    await experimentController.cloneExperiment(mockReq, mockRes);
+
+    expect(experimentInstance.findById).toHaveBeenCalledWith(mockExperiment.id);
+
+    expect(metadataTrackInstance.delete).toHaveBeenCalledWith({ experiment_id: toExperimentId });
+
+    expect(sampleTrackInstance.copyTo)
+      .toHaveBeenCalledWith(mockExperiment.id, toExperimentId, allSampleIds);
+
+    expect(experimentInstance.updateById).toHaveBeenCalledWith(
+      toExperimentId,
+      { samples_order: JSON.stringify(clonedSamplesIds) },
+    );
+
+    expect(mockRes.json).toHaveBeenCalledWith(OK());
+  });
 });

From b31ecbc6df0e29c58ea55f0d58a0f9ebd03bdcf2 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 16:20:35 -0300
Subject: [PATCH 20/29] Add check on any metadata tracks existing before doing
 queries based on them

---
 src/api.v2/model/Sample.js | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/api.v2/model/Sample.js b/src/api.v2/model/Sample.js
index fb79303a9..65cb1dd54 100644
--- a/src/api.v2/model/Sample.js
+++ b/src/api.v2/model/Sample.js
@@ -109,9 +109,12 @@ class Sample extends BasicModel {
     const metadataValueMapRows = [];
 
     await this.sql.transaction(async (trx) => {
-      const metadataTracks = await trx(tableNames.METADATA_TRACK)
-        .insert(metadataTrackKeys.map((key) => ({ experiment_id: toExperimentId, key })))
-        .returning(['id', 'key']);
+      let metadataTracks = [];
+      if (metadataTrackKeys.length > 0) {
+        metadataTracks = await trx(tableNames.METADATA_TRACK)
+          .insert(metadataTrackKeys.map((key) => ({ experiment_id: toExperimentId, key })))
+          .returning(['id', 'key']);
+      }
 
       // Copy each sample in order so
       // the new samples we create follow the same order
@@ -143,8 +146,11 @@ class Sample extends BasicModel {
       });
 
       await trx(tableNames.SAMPLE).insert(sampleRows);
-      await trx(tableNames.SAMPLE_IN_METADATA_TRACK_MAP).insert(metadataValueMapRows);
       await trx(tableNames.SAMPLE_TO_SAMPLE_FILE_MAP).insert(sampleFileMapRows);
+
+      if (metadataValueMapRows.length > 0) {
+        await trx(tableNames.SAMPLE_IN_METADATA_TRACK_MAP).insert(metadataValueMapRows);
+      }
     });
 
     return newSampleIds;

From 6aa021b9bf75886b01779aaa43b02d5e86594bee Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Wed, 22 Jun 2022 16:24:47 -0300
Subject: [PATCH 21/29] Update tests

---
 tests/api.v2/model/Sample.test.js             | 36 ++++++++-
 .../model/__snapshots__/Sample.test.js.snap   | 73 ++++++++++++++++---
 2 files changed, 97 insertions(+), 12 deletions(-)

diff --git a/tests/api.v2/model/Sample.test.js b/tests/api.v2/model/Sample.test.js
index c351a74b3..b32a21c20 100644
--- a/tests/api.v2/model/Sample.test.js
+++ b/tests/api.v2/model/Sample.test.js
@@ -1,4 +1,6 @@
 // @ts-nocheck
+const _ = require('lodash');
+
 const { mockSqlClient, mockTrx } = require('../mocks/getMockSqlClient')();
 
 const Sample = require('../../../src/api.v2/model/Sample');
@@ -68,7 +70,7 @@ describe('model/Sample', () => {
     });
   });
 
-  it('copyTo works correctly if valid params are passed', async () => {
+  it('copyTo works correctly', async () => {
     const fromExperimentId = 'fromExperimentIdMock';
     const toExperimentId = 'toExperimentIdMock';
     const samplesOrder = Object.values(getSamplesResponse).map((sample) => sample.id);
@@ -92,4 +94,36 @@ describe('model/Sample', () => {
     expect(mockTrx.insert.mock.calls).toMatchSnapshot();
     expect(mockTrx.returning.mock.calls).toMatchSnapshot();
   });
+
+  it('copyTo works correctly if experiment has no metadata tracks', async () => {
+    const fromExperimentId = 'fromExperimentIdMock';
+    const toExperimentId = 'toExperimentIdMock';
+
+    const noMetadataGetSamplesResponse = _.cloneDeep(getSamplesResponse);
+    noMetadataGetSamplesResponse.forEach((sample) => {
+      // eslint-disable-next-line no-param-reassign
+      sample.metadata = {};
+    });
+
+    const samplesOrder = Object.values(noMetadataGetSamplesResponse).map((sample) => sample.id);
+
+    mockTrx.returning.mockImplementationOnce(() => Promise.resolve([{ id: 0, key: 'Track0' }]));
+
+    const getSamplesSpy = jest.spyOn(Sample.prototype, 'getSamples')
+      .mockImplementationOnce(() => Promise.resolve(noMetadataGetSamplesResponse));
+
+
+    await new Sample().copyTo(fromExperimentId, toExperimentId, samplesOrder);
+
+
+    expect(getSamplesSpy).toHaveBeenCalledWith(fromExperimentId);
+
+    expect(mockTrx).toHaveBeenCalledWith(tableNames.SAMPLE);
+    expect(mockTrx).toHaveBeenCalledWith(tableNames.SAMPLE_TO_SAMPLE_FILE_MAP);
+    expect(mockTrx).not.toHaveBeenCalledWith(tableNames.METADATA_TRACK);
+    expect(mockTrx).not.toHaveBeenCalledWith(tableNames.SAMPLE_IN_METADATA_TRACK_MAP);
+
+    expect(mockTrx.insert.mock.calls).toMatchSnapshot();
+    expect(mockTrx.returning.mock.calls).toMatchSnapshot();
+  });
 });
diff --git a/tests/api.v2/model/__snapshots__/Sample.test.js.snap b/tests/api.v2/model/__snapshots__/Sample.test.js.snap
index e435474a2..07bf150f8 100644
--- a/tests/api.v2/model/__snapshots__/Sample.test.js.snap
+++ b/tests/api.v2/model/__snapshots__/Sample.test.js.snap
@@ -150,7 +150,7 @@ Array [
 ]
 `;
 
-exports[`model/Sample copyTo works correctly if valid params are passed 1`] = `
+exports[`model/Sample copyTo works correctly 1`] = `
 Array [
   Array [
     Array [
@@ -176,6 +176,34 @@ Array [
       },
     ],
   ],
+  Array [
+    Array [
+      Object {
+        "sample_file_id": "2afe253f-5542-4a90-9fc9-17acdc3ecaf1",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "59b8221d-dd3f-4bb9-ad9d-1166471e7143",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "415323cb-72dc-4f42-b452-c12422ea042f",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "d5c957b9-a6cb-4828-8ee6-1f9da8cacb6a",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "d52a84a8-4669-41b3-a8d1-38e16ddbf522",
+        "sample_id": "mock-uuid",
+      },
+      Object {
+        "sample_file_id": "5b8ec36c-0f06-4a65-b924-da5189c89b7b",
+        "sample_id": "mock-uuid",
+      },
+    ],
+  ],
   Array [
     Array [
       Object {
@@ -190,6 +218,38 @@ Array [
       },
     ],
   ],
+]
+`;
+
+exports[`model/Sample copyTo works correctly 2`] = `
+Array [
+  Array [
+    Array [
+      "id",
+      "key",
+    ],
+  ],
+]
+`;
+
+exports[`model/Sample copyTo works correctly if experiment has no metadata tracks 1`] = `
+Array [
+  Array [
+    Array [
+      Object {
+        "experiment_id": "toExperimentIdMock",
+        "id": "mock-uuid",
+        "name": "KO",
+        "sample_technology": "10x",
+      },
+      Object {
+        "experiment_id": "toExperimentIdMock",
+        "id": "mock-uuid",
+        "name": "WT1",
+        "sample_technology": "10x",
+      },
+    ],
+  ],
   Array [
     Array [
       Object {
@@ -221,13 +281,4 @@ Array [
 ]
 `;
 
-exports[`model/Sample copyTo works correctly if valid params are passed 2`] = `
-Array [
-  Array [
-    Array [
-      "id",
-      "key",
-    ],
-  ],
-]
-`;
+exports[`model/Sample copyTo works correctly if experiment has no metadata tracks 2`] = `Array []`;

From 617410493cc44af9ae76089de1da8a8a56bf236e Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Thu, 23 Jun 2022 11:09:15 -0300
Subject: [PATCH 22/29] Change endpoints based on pols comments

---
 .../controllers/experimentController.js       | 27 +++++++++++--------
 src/api.v2/helpers/roles.js                   |  4 +--
 src/api.v2/model/Experiment.js                | 21 +++++++++++++++
 src/specs/api.v2.yaml                         |  4 +--
 4 files changed, 41 insertions(+), 15 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 6a0f83ae7..30a771db9 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -9,26 +9,25 @@ const sqlClient = require('../../sql/sqlClient');
 
 const getExperimentBackendStatus = require('../helpers/backendStatus/getExperimentBackendStatus');
 const Sample = require('../model/Sample');
-const MetadataTrack = require('../model/MetadataTrack');
 
 const logger = getLogger('[ExperimentController] - ');
 
 const getAllExperiments = async (req, res) => {
   const { user: { sub: userId } } = req;
-  console.log(`Getting all experiments for user: ${userId}`);
+  logger.log(`Getting all experiments for user: ${userId}`);
 
   const data = await new Experiment().getAllExperiments(userId);
 
-  console.log(`Finished getting all experiments for user: ${userId}, length: ${data.length}`);
+  logger.log(`Finished getting all experiments for user: ${userId}, length: ${data.length}`);
   res.json(data);
 };
 
 const getAllExampleExperiments = async (req, res) => {
-  console.log('Getting example experiments');
+  logger.log('Getting example experiments');
 
   const data = await new Experiment().getAllExampleExperiments();
 
-  console.log(`Finished getting example experiments, length: ${data.length}`);
+  logger.log(`Finished getting example experiments, length: ${data.length}`);
   res.json(data);
 };
 
@@ -151,15 +150,21 @@ const cloneExperiment = async (req, res) => {
   };
 
   const {
-    params: { experimentId: fromExperimentId, toExperimentId },
+    params: { experimentId: fromExperimentId },
     body: { samplesSubsetIds = await getAllSampleIds(fromExperimentId) },
+    user: { sub: userId },
   } = req;
 
-  logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
+  logger.log(`Creating experiment to clone ${fromExperimentId} to`);
+
+  let toExperimentId;
 
-  // toExperiment might be an old experiment with metadata tracks,
-  // we want to start without any old tracks so clear them out
-  await new MetadataTrack().delete({ experiment_id: toExperimentId });
+  await sqlClient.get().transaction(async (trx) => {
+    toExperimentId = await new Experiment(trx).copyFrom(fromExperimentId);
+    await new UserAccess(trx).createNewExperimentPermissions(userId, toExperimentId);
+  });
+
+  logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
 
   const clonedSamplesOrder = await new Sample()
     .copyTo(fromExperimentId, toExperimentId, samplesSubsetIds);
@@ -171,7 +176,7 @@ const cloneExperiment = async (req, res) => {
 
   logger.log(`Finished cloning experiment ${fromExperimentId}, new expeirment's id is ${toExperimentId}`);
 
-  res.json(OK());
+  res.json(toExperimentId);
 };
 
 module.exports = {
diff --git a/src/api.v2/helpers/roles.js b/src/api.v2/helpers/roles.js
index 653caadb4..d3aa051b0 100644
--- a/src/api.v2/helpers/roles.js
+++ b/src/api.v2/helpers/roles.js
@@ -18,10 +18,10 @@ const allowedResources = {
     'socket',
     '/experiments/(?<experimentId>.*)/plots-tables/(?<plotUuid>.*)',
     '/experiments/(?<experimentId>.*)/cellSets',
-    '/experiments/(?<experimentId>.*)/clone/.*',
+    '/experiments/(?<experimentId>.*)/clone',
   ],
   [VIEWER]: [
-    '/experiments/(?<experimentId>.*)/clone/.*',
+    '/experiments/(?<experimentId>.*)/clone',
   ],
 };
 const isRoleAuthorized = (role, resource, method) => {
diff --git a/src/api.v2/model/Experiment.js b/src/api.v2/model/Experiment.js
index c6f7dc339..4fde73e0d 100644
--- a/src/api.v2/model/Experiment.js
+++ b/src/api.v2/model/Experiment.js
@@ -1,4 +1,5 @@
 const _ = require('lodash');
+const { v4: uuidv4 } = require('uuid');
 
 const BasicModel = require('./BasicModel');
 const sqlClient = require('../../sql/sqlClient');
@@ -105,6 +106,26 @@ class Experiment extends BasicModel {
     return result;
   }
 
+  async copyFrom(fromExperimentId) {
+    const toExperimentId = uuidv4().replace(/-/g, '');
+
+    const { sql } = this;
+
+    await sql
+      .insert(
+        sql(tableNames.EXPERIMENT)
+          .select(
+            sql.raw('? as id', [toExperimentId]),
+            'name',
+            'description',
+          )
+          .where({ id: fromExperimentId }),
+      )
+      .into(sql.raw(`${tableNames.EXPERIMENT} (id, name, description)`));
+
+    return toExperimentId;
+  }
+
   // Sets samples_order as an array that has the sample in oldPosition moved to newPosition
   async updateSamplePosition(
     experimentId, oldPosition, newPosition,
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index 47e1c8105..dcda7e684 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -1186,7 +1186,7 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
-  '/experiments/{experimentId}/clone/{toExperimentId}':
+  '/experiments/{experimentId}/clone':
     post:
       summary: Clone an experiment
       description: Clone an experiment, returns the id of the new experiment
@@ -1211,7 +1211,7 @@ paths:
           content:
             application/json:
               schema:
-                $ref: '#/components/schemas/HTTPSuccess'
+                type: string
         '400':
           description: Bad Request
           content:

From 5d6c8419d35872bd1e14b11253c8fb8686ef4129 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Thu, 23 Jun 2022 11:22:07 -0300
Subject: [PATCH 23/29] Update tests

---
 .../controllers/experimentController.js       |  2 +-
 src/api.v2/model/Experiment.js                |  2 +-
 src/api.v2/model/__mocks__/Experiment.js      |  1 +
 .../controllers/experimentController.test.js  | 34 +++++++++++++------
 tests/api.v2/routes/experiment.test.js        |  9 ++---
 5 files changed, 30 insertions(+), 18 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 30a771db9..653b98c99 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -160,7 +160,7 @@ const cloneExperiment = async (req, res) => {
   let toExperimentId;
 
   await sqlClient.get().transaction(async (trx) => {
-    toExperimentId = await new Experiment(trx).copyFrom(fromExperimentId);
+    toExperimentId = await new Experiment(trx).createCopy(fromExperimentId);
     await new UserAccess(trx).createNewExperimentPermissions(userId, toExperimentId);
   });
 
diff --git a/src/api.v2/model/Experiment.js b/src/api.v2/model/Experiment.js
index 4fde73e0d..9ad08172e 100644
--- a/src/api.v2/model/Experiment.js
+++ b/src/api.v2/model/Experiment.js
@@ -106,7 +106,7 @@ class Experiment extends BasicModel {
     return result;
   }
 
-  async copyFrom(fromExperimentId) {
+  async createCopy(fromExperimentId) {
     const toExperimentId = uuidv4().replace(/-/g, '');
 
     const { sql } = this;
diff --git a/src/api.v2/model/__mocks__/Experiment.js b/src/api.v2/model/__mocks__/Experiment.js
index 2df9fe5aa..38245efc9 100644
--- a/src/api.v2/model/__mocks__/Experiment.js
+++ b/src/api.v2/model/__mocks__/Experiment.js
@@ -6,6 +6,7 @@ const stub = {
   updateSamplePosition: jest.fn(),
   updateProcessingConfig: jest.fn(),
   getProcessingConfig: jest.fn(),
+  createCopy: jest.fn(),
   addSample: jest.fn(),
   deleteSample: jest.fn(),
   getDownloadLink: jest.fn(),
diff --git a/tests/api.v2/controllers/experimentController.test.js b/tests/api.v2/controllers/experimentController.test.js
index 674abcef6..f7e432da3 100644
--- a/tests/api.v2/controllers/experimentController.test.js
+++ b/tests/api.v2/controllers/experimentController.test.js
@@ -288,16 +288,18 @@ describe('experimentController', () => {
   });
 
   it('cloneExperiment works correctly when samplesSubsetIds is provided', async () => {
-    const toExperimentId = 'toExperimentIdMock';
     const samplesSubsetIds = ['mockSample2', 'mockSample3'];
     const clonedSamplesSubsetIds = ['mockClonedSample2', 'mockClonedSample3'];
+    const userId = 'mockUserId';
+    const toExperimentId = 'mockToExperimentId';
 
     const mockReq = {
-      params: { experimentId: mockExperiment.id, toExperimentId },
+      params: { experimentId: mockExperiment.id },
       body: { samplesSubsetIds },
+      user: { sub: userId },
     };
 
-    metadataTrackInstance.delete.mockImplementationOnce(() => Promise.resolve());
+    experimentInstance.createCopy.mockImplementationOnce(() => Promise.resolve(toExperimentId));
     sampleTrackInstance.copyTo.mockImplementationOnce(
       () => Promise.resolve(clonedSamplesSubsetIds),
     );
@@ -305,33 +307,40 @@ describe('experimentController', () => {
 
     await experimentController.cloneExperiment(mockReq, mockRes);
 
-    expect(metadataTrackInstance.delete).toHaveBeenCalledWith({ experiment_id: toExperimentId });
+    // Creates new experiment
+    expect(experimentInstance.createCopy).toHaveBeenCalledWith(mockExperiment.id);
+    expect(userAccessInstance.createNewExperimentPermissions)
+      .toHaveBeenCalledWith(userId, toExperimentId);
 
+    // Creates copy samples for new experiment
     expect(sampleTrackInstance.copyTo)
       .toHaveBeenCalledWith(mockExperiment.id, toExperimentId, samplesSubsetIds);
 
+    // Sets created sample in experiment
     expect(experimentInstance.updateById).toHaveBeenCalledWith(
       toExperimentId,
       { samples_order: JSON.stringify(clonedSamplesSubsetIds) },
     );
 
-    expect(mockRes.json).toHaveBeenCalledWith(OK());
+    expect(mockRes.json).toHaveBeenCalledWith(toExperimentId);
   });
 
   it('cloneExperiment works correctly when samplesSubsetIds is NOT provided', async () => {
-    const toExperimentId = 'toExperimentIdMock';
     const allSampleIds = ['mockSample1', 'mockSample2', 'mockSample3', 'mockSample4'];
     const clonedSamplesIds = ['mockClonedSample1', 'mockClonedSample2', 'mockClonedSample3', 'mockClonedSample4'];
+    const userId = 'mockUserId';
+    const toExperimentId = 'mockToExperimentId';
 
     const mockReq = {
-      params: { experimentId: mockExperiment.id, toExperimentId },
+      params: { experimentId: mockExperiment.id },
       body: {},
+      user: { sub: userId },
     };
 
+    experimentInstance.createCopy.mockImplementationOnce(() => Promise.resolve(toExperimentId));
     experimentInstance.findById.mockReturnValueOnce(
       { first: () => Promise.resolve({ samplesOrder: allSampleIds }) },
     );
-    metadataTrackInstance.delete.mockImplementationOnce(() => Promise.resolve());
     sampleTrackInstance.copyTo.mockImplementationOnce(
       () => Promise.resolve(clonedSamplesIds),
     );
@@ -341,16 +350,21 @@ describe('experimentController', () => {
 
     expect(experimentInstance.findById).toHaveBeenCalledWith(mockExperiment.id);
 
-    expect(metadataTrackInstance.delete).toHaveBeenCalledWith({ experiment_id: toExperimentId });
+    // Creates new experiment
+    expect(experimentInstance.createCopy).toHaveBeenCalledWith(mockExperiment.id);
+    expect(userAccessInstance.createNewExperimentPermissions)
+      .toHaveBeenCalledWith(userId, toExperimentId);
 
+    // Creates copy samples for new experiment
     expect(sampleTrackInstance.copyTo)
       .toHaveBeenCalledWith(mockExperiment.id, toExperimentId, allSampleIds);
 
+    // Sets created sample in experiment
     expect(experimentInstance.updateById).toHaveBeenCalledWith(
       toExperimentId,
       { samples_order: JSON.stringify(clonedSamplesIds) },
     );
 
-    expect(mockRes.json).toHaveBeenCalledWith(OK());
+    expect(mockRes.json).toHaveBeenCalledWith(toExperimentId);
   });
 });
diff --git a/tests/api.v2/routes/experiment.test.js b/tests/api.v2/routes/experiment.test.js
index 0f7cb4629..90d0db22a 100644
--- a/tests/api.v2/routes/experiment.test.js
+++ b/tests/api.v2/routes/experiment.test.js
@@ -337,7 +337,6 @@ describe('tests for experiment route', () => {
 
   it('cloneExperiment results in a successful response without a body', async (done) => {
     const experimentId = 'fromExperimentId';
-    const toExperimentId = 'toExperimentId';
 
     experimentController.cloneExperiment.mockImplementationOnce((req, res) => {
       res.json(OK());
@@ -345,7 +344,7 @@ describe('tests for experiment route', () => {
     });
 
     request(app)
-      .post(`/v2/experiments/${experimentId}/clone/${toExperimentId}`)
+      .post(`/v2/experiments/${experimentId}/clone`)
       .set({ 'Content-Type': 'application/json' })
       .expect(200)
       .end((err) => {
@@ -360,7 +359,6 @@ describe('tests for experiment route', () => {
 
   it('cloneExperiment results in a successful response with a valid body', async (done) => {
     const experimentId = 'fromExperimentId';
-    const toExperimentId = 'toExperimentId';
 
     const body = { samplesSubsetIds: ['sampleId1', 'sampleId2'] };
 
@@ -370,7 +368,7 @@ describe('tests for experiment route', () => {
     });
 
     request(app)
-      .post(`/v2/experiments/${experimentId}/clone/${toExperimentId}`)
+      .post(`/v2/experiments/${experimentId}/clone`)
       .send(body)
       .expect(200)
       .end((err) => {
@@ -385,7 +383,6 @@ describe('tests for experiment route', () => {
 
   it('cloneExperiment results in a 400 with an invalid body', async (done) => {
     const experimentId = 'fromExperimentId';
-    const toExperimentId = 'toExperimentId';
 
     const body = { samplesSubsetIdsInvalid: ['sampleId1', 'sampleId2'] };
 
@@ -395,7 +392,7 @@ describe('tests for experiment route', () => {
     });
 
     request(app)
-      .post(`/v2/experiments/${experimentId}/clone/${toExperimentId}`)
+      .post(`/v2/experiments/${experimentId}/clone`)
       .send(body)
       .expect(400)
       .end((err) => {

From 61f91ea74b5173ef83d714c6b374642b698a05e7 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Thu, 23 Jun 2022 13:01:55 -0300
Subject: [PATCH 24/29] Rename to fromSamples

---
 src/api.v2/model/Sample.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/api.v2/model/Sample.js b/src/api.v2/model/Sample.js
index 65cb1dd54..58f5c9dfc 100644
--- a/src/api.v2/model/Sample.js
+++ b/src/api.v2/model/Sample.js
@@ -98,11 +98,11 @@ class Sample extends BasicModel {
    * @param {*} toExperimentId
    */
   async copyTo(fromExperimentId, toExperimentId, samplesOrder) {
-    const result = await this.getSamples(fromExperimentId);
+    const fromSamples = await this.getSamples(fromExperimentId);
 
     const newSampleIds = [];
 
-    const metadataTrackKeys = Object.keys(result[0].metadata);
+    const metadataTrackKeys = Object.keys(fromSamples[0].metadata);
 
     const sampleRows = [];
     const sampleFileMapRows = [];
@@ -119,7 +119,7 @@ class Sample extends BasicModel {
       // Copy each sample in order so
       // the new samples we create follow the same order
       samplesOrder.forEach((fromSampleId) => {
-        const sample = result.find(({ id }) => id === fromSampleId);
+        const sample = fromSamples.find(({ id }) => id === fromSampleId);
 
         const toSampleId = uuidv4();
 

From 63b282dba65c5f2ecb16e53a4cb691094f8a956b Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Thu, 23 Jun 2022 13:05:04 -0300
Subject: [PATCH 25/29] Rename

---
 src/api.v2/controllers/experimentController.js        | 6 +++---
 src/api.v2/model/Experiment.js                        | 2 +-
 src/api.v2/model/__mocks__/Experiment.js              | 2 +-
 src/api.v2/routes/experiment.js                       | 6 +++---
 src/specs/api.v2.yaml                                 | 4 ++--
 tests/api.v2/controllers/experimentController.test.js | 8 ++++----
 tests/api.v2/model/Experiment.test.js                 | 4 ++--
 tests/api.v2/routes/experiment.test.js                | 6 +++---
 8 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 653b98c99..8c78822fe 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -22,10 +22,10 @@ const getAllExperiments = async (req, res) => {
   res.json(data);
 };
 
-const getAllExampleExperiments = async (req, res) => {
+const getExampleExperiments = async (req, res) => {
   logger.log('Getting example experiments');
 
-  const data = await new Experiment().getAllExampleExperiments();
+  const data = await new Experiment().getExampleExperiments();
 
   logger.log(`Finished getting example experiments, length: ${data.length}`);
   res.json(data);
@@ -181,7 +181,7 @@ const cloneExperiment = async (req, res) => {
 
 module.exports = {
   getAllExperiments,
-  getAllExampleExperiments,
+  getExampleExperiments,
   getExperiment,
   createExperiment,
   updateProcessingConfig,
diff --git a/src/api.v2/model/Experiment.js b/src/api.v2/model/Experiment.js
index 9ad08172e..16b9d9bc9 100644
--- a/src/api.v2/model/Experiment.js
+++ b/src/api.v2/model/Experiment.js
@@ -61,7 +61,7 @@ class Experiment extends BasicModel {
     return result;
   }
 
-  async getAllExampleExperiments() {
+  async getExampleExperiments() {
     return this.getAllExperiments(constants.PUBLIC_ACCESS_ID);
   }
 
diff --git a/src/api.v2/model/__mocks__/Experiment.js b/src/api.v2/model/__mocks__/Experiment.js
index 38245efc9..50707c8d3 100644
--- a/src/api.v2/model/__mocks__/Experiment.js
+++ b/src/api.v2/model/__mocks__/Experiment.js
@@ -10,7 +10,7 @@ const stub = {
   addSample: jest.fn(),
   deleteSample: jest.fn(),
   getDownloadLink: jest.fn(),
-  getAllExampleExperiments: jest.fn(),
+  getExampleExperiments: jest.fn(),
   ...BasicModel,
 };
 
diff --git a/src/api.v2/routes/experiment.js b/src/api.v2/routes/experiment.js
index c2a99d07c..eb484f280 100644
--- a/src/api.v2/routes/experiment.js
+++ b/src/api.v2/routes/experiment.js
@@ -1,5 +1,5 @@
 const {
-  getAllExperiments, getAllExampleExperiments,
+  getAllExperiments, getExampleExperiments,
   createExperiment, getExperiment, patchExperiment, deleteExperiment, cloneExperiment,
   getProcessingConfig, updateProcessingConfig,
   updateSamplePosition,
@@ -13,9 +13,9 @@ module.exports = {
     expressAuthenticationOnlyMiddleware,
     (req, res, next) => getAllExperiments(req, res).catch(next),
   ],
-  'experiment#getAllExampleExperiments': [
+  'experiment#getExampleExperiments': [
     expressAuthenticationOnlyMiddleware,
-    (req, res, next) => getAllExampleExperiments(req, res).catch(next),
+    (req, res, next) => getExampleExperiments(req, res).catch(next),
   ],
   'experiment#getExperiment': [
     expressAuthorizationMiddleware,
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index dcda7e684..b3f657812 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -266,8 +266,8 @@ paths:
     get:
       summary: Get all example experiments
       description: Get all experiments that are for demonstration
-      operationId: getAllExampleExperiments
-      x-eov-operation-id: experiment#getAllExampleExperiments
+      operationId: getExampleExperiments
+      x-eov-operation-id: experiment#getExampleExperiments
       x-eov-operation-handler: routes/experiment
       responses:
         '200':
diff --git a/tests/api.v2/controllers/experimentController.test.js b/tests/api.v2/controllers/experimentController.test.js
index f7e432da3..df442630e 100644
--- a/tests/api.v2/controllers/experimentController.test.js
+++ b/tests/api.v2/controllers/experimentController.test.js
@@ -77,16 +77,16 @@ describe('experimentController', () => {
     expect(mockRes.json).toHaveBeenCalledWith(getAllExperimentsResponse);
   });
 
-  it('getAllExampleExperiments works correctly', async () => {
+  it('getExampleExperiments works correctly', async () => {
     const mockReq = { user: { sub: 'mockUserId' } };
 
-    experimentInstance.getAllExampleExperiments.mockImplementationOnce(
+    experimentInstance.getExampleExperiments.mockImplementationOnce(
       () => Promise.resolve(getAllExperimentsResponse),
     );
 
-    await experimentController.getAllExampleExperiments(mockReq, mockRes);
+    await experimentController.getExampleExperiments(mockReq, mockRes);
 
-    expect(experimentInstance.getAllExampleExperiments).toHaveBeenCalled();
+    expect(experimentInstance.getExampleExperiments).toHaveBeenCalled();
     expect(mockRes.json).toHaveBeenCalledWith(getAllExperimentsResponse);
   });
 
diff --git a/tests/api.v2/model/Experiment.test.js b/tests/api.v2/model/Experiment.test.js
index 1a0722b04..4831531ee 100644
--- a/tests/api.v2/model/Experiment.test.js
+++ b/tests/api.v2/model/Experiment.test.js
@@ -60,13 +60,13 @@ describe('model/Experiment', () => {
     expect(mockSqlClient.as).toHaveBeenCalledWith('mainQuery');
   });
 
-  it('getAllExampleExperiments works correctly', async () => {
+  it('getExampleExperiments works correctly', async () => {
     const expectedResult = { isMockResult: true };
 
     const getAllExperimentsSpy = jest.spyOn(Experiment.prototype, 'getAllExperiments')
       .mockImplementationOnce(() => Promise.resolve(expectedResult));
 
-    const result = await new Experiment().getAllExampleExperiments('mockUserId');
+    const result = await new Experiment().getExampleExperiments('mockUserId');
 
     expect(result).toBe(expectedResult);
     expect(getAllExperimentsSpy).toHaveBeenCalledWith(constants.PUBLIC_ACCESS_ID);
diff --git a/tests/api.v2/routes/experiment.test.js b/tests/api.v2/routes/experiment.test.js
index 90d0db22a..a2ef84ae7 100644
--- a/tests/api.v2/routes/experiment.test.js
+++ b/tests/api.v2/routes/experiment.test.js
@@ -22,7 +22,7 @@ jest.mock('../../../src/api.v2/controllers/experimentController', () => ({
   getProcessingConfig: jest.fn(),
   updateProcessingConfig: jest.fn(),
   downloadData: jest.fn(),
-  getAllExampleExperiments: jest.fn(),
+  getExampleExperiments: jest.fn(),
   cloneExperiment: jest.fn(),
 }));
 
@@ -316,8 +316,8 @@ describe('tests for experiment route', () => {
       });
   });
 
-  it('getAllExampleExperiments results in a successful response', async (done) => {
-    experimentController.getAllExampleExperiments.mockImplementationOnce((req, res) => {
+  it('getExampleExperiments results in a successful response', async (done) => {
+    experimentController.getExampleExperiments.mockImplementationOnce((req, res) => {
       res.json(getExperimentResponse);
       return Promise.resolve();
     });

From efd9f6cee9b42f90f24cca8a16361a090735cb08 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Thu, 23 Jun 2022 13:05:26 -0300
Subject: [PATCH 26/29] Fix comment

---
 src/api.v2/model/Sample.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/api.v2/model/Sample.js b/src/api.v2/model/Sample.js
index 58f5c9dfc..986ba65be 100644
--- a/src/api.v2/model/Sample.js
+++ b/src/api.v2/model/Sample.js
@@ -92,7 +92,7 @@ class Sample extends BasicModel {
   }
 
   /**
-   * Creates copy samples from one experiment to another one
+   * Copies samples from one experiment to another one
    *
    * @param {*} fromExperimentId
    * @param {*} toExperimentId

From c9426d4b9bd38120343dfe0d66c09dddbe89ff41 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Thu, 23 Jun 2022 13:06:18 -0300
Subject: [PATCH 27/29] Refactor

---
 src/api.v2/model/Experiment.js | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/api.v2/model/Experiment.js b/src/api.v2/model/Experiment.js
index 16b9d9bc9..2fef75145 100644
--- a/src/api.v2/model/Experiment.js
+++ b/src/api.v2/model/Experiment.js
@@ -46,13 +46,17 @@ class Experiment extends BasicModel {
 
     const aliasedExperimentFields = fields.map((field) => `e.${field}`);
 
+    const mainQuery = this.sql
+      .select([...aliasedExperimentFields, 'm.key'])
+      .from(tableNames.USER_ACCESS)
+      .where('user_id', userId)
+      .join(`${tableNames.EXPERIMENT} as e`, 'e.id', `${tableNames.USER_ACCESS}.experiment_id`)
+      .leftJoin(`${tableNames.METADATA_TRACK} as m`, 'e.id', 'm.experiment_id')
+      .as('mainQuery');
+
     const result = await collapseKeyIntoArray(
-      this.sql.select([...aliasedExperimentFields, 'm.key'])
-        .from(tableNames.USER_ACCESS)
-        .where('user_id', userId)
-        .join(`${tableNames.EXPERIMENT} as e`, 'e.id', `${tableNames.USER_ACCESS}.experiment_id`)
-        .leftJoin(`${tableNames.METADATA_TRACK} as m`, 'e.id', 'm.experiment_id')
-        .as('mainQuery'), [...fields],
+      mainQuery,
+      [...fields],
       'key',
       'metadataKeys',
       this.sql,

From c2b71d2dfb62f9a27fea977e05a99bee66afeabf Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Thu, 23 Jun 2022 13:07:29 -0300
Subject: [PATCH 28/29] Rename

---
 src/api.v2/controllers/experimentController.js        |  4 ++--
 src/specs/api.v2.yaml                                 |  4 ++--
 tests/api.v2/controllers/experimentController.test.js | 10 +++++-----
 tests/api.v2/routes/experiment.test.js                |  2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 8c78822fe..5fab7c08e 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -151,7 +151,7 @@ const cloneExperiment = async (req, res) => {
 
   const {
     params: { experimentId: fromExperimentId },
-    body: { samplesSubsetIds = await getAllSampleIds(fromExperimentId) },
+    body: { samplesToCloneIds = await getAllSampleIds(fromExperimentId) },
     user: { sub: userId },
   } = req;
 
@@ -167,7 +167,7 @@ const cloneExperiment = async (req, res) => {
   logger.log(`Cloning experiment ${fromExperimentId} into ${toExperimentId}`);
 
   const clonedSamplesOrder = await new Sample()
-    .copyTo(fromExperimentId, toExperimentId, samplesSubsetIds);
+    .copyTo(fromExperimentId, toExperimentId, samplesToCloneIds);
 
   await new Experiment().updateById(
     toExperimentId,
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index b3f657812..1f39116eb 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -1197,10 +1197,10 @@ paths:
         content:
           application/json:
             schema:
-              description: If samplesSubsetIds is sent then the cloned experiment only contains the subset samples instead of all of them
+              description: If samplesToCloneIds is sent then the cloned experiment only contains the subset samples instead of all of them
               type: object
               properties:
-                samplesSubsetIds:
+                samplesToCloneIds:
                   type: array
                   items:
                     type: string   
diff --git a/tests/api.v2/controllers/experimentController.test.js b/tests/api.v2/controllers/experimentController.test.js
index df442630e..7e696a138 100644
--- a/tests/api.v2/controllers/experimentController.test.js
+++ b/tests/api.v2/controllers/experimentController.test.js
@@ -287,15 +287,15 @@ describe('experimentController', () => {
       .toHaveBeenCalledWith(mockExperiment.id, bucketNames.PROCESSED_MATRIX);
   });
 
-  it('cloneExperiment works correctly when samplesSubsetIds is provided', async () => {
-    const samplesSubsetIds = ['mockSample2', 'mockSample3'];
+  it('cloneExperiment works correctly when samplesToCloneIds is provided', async () => {
+    const samplesToCloneIds = ['mockSample2', 'mockSample3'];
     const clonedSamplesSubsetIds = ['mockClonedSample2', 'mockClonedSample3'];
     const userId = 'mockUserId';
     const toExperimentId = 'mockToExperimentId';
 
     const mockReq = {
       params: { experimentId: mockExperiment.id },
-      body: { samplesSubsetIds },
+      body: { samplesToCloneIds },
       user: { sub: userId },
     };
 
@@ -314,7 +314,7 @@ describe('experimentController', () => {
 
     // Creates copy samples for new experiment
     expect(sampleTrackInstance.copyTo)
-      .toHaveBeenCalledWith(mockExperiment.id, toExperimentId, samplesSubsetIds);
+      .toHaveBeenCalledWith(mockExperiment.id, toExperimentId, samplesToCloneIds);
 
     // Sets created sample in experiment
     expect(experimentInstance.updateById).toHaveBeenCalledWith(
@@ -325,7 +325,7 @@ describe('experimentController', () => {
     expect(mockRes.json).toHaveBeenCalledWith(toExperimentId);
   });
 
-  it('cloneExperiment works correctly when samplesSubsetIds is NOT provided', async () => {
+  it('cloneExperiment works correctly when samplesToCloneIds is NOT provided', async () => {
     const allSampleIds = ['mockSample1', 'mockSample2', 'mockSample3', 'mockSample4'];
     const clonedSamplesIds = ['mockClonedSample1', 'mockClonedSample2', 'mockClonedSample3', 'mockClonedSample4'];
     const userId = 'mockUserId';
diff --git a/tests/api.v2/routes/experiment.test.js b/tests/api.v2/routes/experiment.test.js
index a2ef84ae7..6551d62c2 100644
--- a/tests/api.v2/routes/experiment.test.js
+++ b/tests/api.v2/routes/experiment.test.js
@@ -360,7 +360,7 @@ describe('tests for experiment route', () => {
   it('cloneExperiment results in a successful response with a valid body', async (done) => {
     const experimentId = 'fromExperimentId';
 
-    const body = { samplesSubsetIds: ['sampleId1', 'sampleId2'] };
+    const body = { samplesToCloneIds: ['sampleId1', 'sampleId2'] };
 
     experimentController.cloneExperiment.mockImplementationOnce((req, res) => {
       res.json(OK());

From 9040c9a34d843ab3649bbfd1a29aa3f265dae2ea Mon Sep 17 00:00:00 2001
From: Martin Fosco <cosa65@users.noreply.github.com>
Date: Thu, 23 Jun 2022 14:10:47 -0300
Subject: [PATCH 29/29] Update experimentController.js

---
 src/api.v2/controllers/experimentController.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/api.v2/controllers/experimentController.js b/src/api.v2/controllers/experimentController.js
index 5fab7c08e..62882a7e0 100644
--- a/src/api.v2/controllers/experimentController.js
+++ b/src/api.v2/controllers/experimentController.js
@@ -174,7 +174,7 @@ const cloneExperiment = async (req, res) => {
     { samples_order: JSON.stringify(clonedSamplesOrder) },
   );
 
-  logger.log(`Finished cloning experiment ${fromExperimentId}, new expeirment's id is ${toExperimentId}`);
+  logger.log(`Finished cloning experiment ${fromExperimentId}, new experiment's id is ${toExperimentId}`);
 
   res.json(toExperimentId);
 };