Merge branch '55-update-scripts-api' into 'dev'

Resolve "Update scripts to use new `PUT` and `POST` to populate database"

Closes #55

See merge request !14

.gitignore

+.DS_Store
 __pycache__/
 *.egg-info/
-.env
+*.env
 .env_dev
 .idea/
 .vscode
@@ -18,3 +19,4 @@ notebooks/
 
 # Tests files
 .coverage
+.pytest_cache

README.md

 # Metagenedb
 
-[![pipeline status](https://gitlab.pasteur.fr/metagenomics/metagenedb/badges/master/pipeline.svg)](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/master)
-[![coverage report](https://gitlab.pasteur.fr/metagenomics/metagenedb/badges/master/coverage.svg)](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/master)
+[![pipeline status](https://gitlab.pasteur.fr/metagenomics/metagenedb/badges/dev/pipeline.svg)](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/dev)
+[![coverage report](https://gitlab.pasteur.fr/metagenomics/metagenedb/badges/dev/coverage.svg)](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/dev)
 
 Django based project to build genes catalog and tools
 to play with it and contact external services.

backend/Pipfile

@@ -27,6 +27,7 @@ Cycler = "*"
 jupyter = "*"
 factory-boy = "*"
 pytest-factoryboy = "*"
+pylint = "*"
 
 [packages]
 certifi = "*"

backend/Pipfile.lock

 {
     "_meta": {
         "hash": {
-            "sha256": "ccf8681e4b40107fa82f5be41d08cd73348d3b3ebc0fdbad1a18dbf549297337"
+            "sha256": "a9a2ecd17c88a47e5a54273aab5c3fae726014e859e07586f49446d8fa886911"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -25,11 +25,11 @@
         },
         "certifi": {
             "hashes": [
-                "sha256:046832c04d4e752f37383b628bc601a7ea7211496b4638f6514d0e5b9acc4939",
-                "sha256:945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695"
+                "sha256:e4f3620cfea4f83eedc95b24abd9cd56f3c4b146dd0177e83a21b4eb49e21e50",
+                "sha256:fd7c7c74727ddcf00e9acd26bba8da604ffec95bf1c2144e67aff7a8b50e6cef"
             ],
             "index": "pypi",
-            "version": "==2019.6.16"
+            "version": "==2019.9.11"
         },
         "chardet": {
             "hashes": [
@@ -179,7 +179,7 @@
         },
         "master": {
             "git": "https://github.com/khillion/bioapi.git",
-            "ref": "201003535ff7b788492f056884b1ad166ee02b59"
+            "ref": "1b0f58f458ed5c3b8d0a5f6cdc9a7838d52e52fe"
         },
         "metagenedb": {
             "editable": true,
@@ -187,25 +187,25 @@
         },
         "numpy": {
             "hashes": [
-                "sha256:03f2ebcbffcce2dec8860633b89a93e80c6a239d21a77ae8b241450dc21e8c35",
-                "sha256:078c8025da5ab9e8657edc9c2a1e9642e06e953bc7baa2e65c1aa9d9dfb7e98b",
-                "sha256:0fbfa98c5d5c3c6489cc1e852ec94395d51f35d9ebe70c6850e47f465038cdf4",
-                "sha256:1c841033f4fe6801648180c3033c45b3235a8bbd09bc7249010f99ea27bb6790",
-                "sha256:2c0984a01ddd0aeec89f0ce46ef21d64761048cd76c0074d0658c91f9131f154",
-                "sha256:4c166dcb0fff7cb3c0bbc682dfb5061852a2547efb6222e043a7932828c08fb5",
-                "sha256:8c2d98d0623bd63fb883b65256c00454d5f53127a5a7bcdaa8bdc582814e8cb4",
-                "sha256:8cb4b6ae45aad6d26712a1ce0a3f2556c5e1484867f9649e03496e45d6a5eba4",
-                "sha256:93050e73c446c82065b7410221b07682e475ac51887cd9368227a5d944afae80",
-                "sha256:a3f6b3024f8826d8b1490e6e2a9b99e841cd2c375791b1df62991bd8f4c00b89",
-                "sha256:bede70fd8699695363f39e86c1e869b2c8b74fb5ef135a67b9e1eeebff50322a",
-                "sha256:c304b2221f33489cd15a915237a84cdfe9420d7e4d4828c78a0820f9d990395c",
-                "sha256:f11331530f0eff69a758d62c2461cd98cdc2eae0147279d8fc86e0464eb7e8ca",
-                "sha256:fa5f2a8ef1e07ba258dc07d4dd246de23ef4ab920ae0f3fa2a1cc5e90f0f1888",
-                "sha256:fb6178b0488b0ce6a54bc4accbdf5225e937383586555604155d64773f6beb2b",
-                "sha256:fd5e830d4dc31658d61a6452cd3e842213594d8c15578cdae6829e36ad9c0930"
-            ],
-            "index": "pypi",
-            "version": "==1.17.1"
+                "sha256:05dbfe72684cc14b92568de1bc1f41e5f62b00f714afc9adee42f6311738091f",
+                "sha256:0d82cb7271a577529d07bbb05cb58675f2deb09772175fab96dc8de025d8ac05",
+                "sha256:10132aa1fef99adc85a905d82e8497a580f83739837d7cbd234649f2e9b9dc58",
+                "sha256:12322df2e21f033a60c80319c25011194cd2a21294cc66fee0908aeae2c27832",
+                "sha256:16f19b3aa775dddc9814e02a46b8e6ae6a54ed8cf143962b4e53f0471dbd7b16",
+                "sha256:3d0b0989dd2d066db006158de7220802899a1e5c8cf622abe2d0bd158fd01c2c",
+                "sha256:438a3f0e7b681642898fd7993d38e2bf140a2d1eafaf3e89bb626db7f50db355",
+                "sha256:5fd214f482ab53f2cea57414c5fb3e58895b17df6e6f5bca5be6a0bb6aea23bb",
+                "sha256:73615d3edc84dd7c4aeb212fa3748fb83217e00d201875a47327f55363cef2df",
+                "sha256:7bd355ad7496f4ce1d235e9814ec81ee3d28308d591c067ce92e49f745ba2c2f",
+                "sha256:7d077f2976b8f3de08a0dcf5d72083f4af5411e8fddacd662aae27baa2601196",
+                "sha256:a4092682778dc48093e8bda8d26ee8360153e2047826f95a3f5eae09f0ae3abf",
+                "sha256:b458de8624c9f6034af492372eb2fee41a8e605f03f4732f43fc099e227858b2",
+                "sha256:e70fc8ff03a961f13363c2c95ef8285e0cf6a720f8271836f852cc0fa64e97c8",
+                "sha256:ee8e9d7cad5fe6dde50ede0d2e978d81eafeaa6233fb0b8719f60214cf226578",
+                "sha256:f4a4f6aba148858a5a5d546a99280f71f5ee6ec8182a7d195af1a914195b21a2"
+            ],
+            "index": "pypi",
+            "version": "==1.17.2"
         },
         "packaging": {
             "hashes": [
@@ -379,6 +379,13 @@
             "markers": "sys_platform == 'darwin'",
             "version": "==0.1.0"
         },
+        "astroid": {
+            "hashes": [
+                "sha256:6560e1e1749f68c64a4b5dee4e091fce798d2f0d84ebe638cf0e0585a343acf4",
+                "sha256:b65db1bbaac9f9f4d190199bb8680af6f6f84fd3769a5ea883df8a91fe68b4c4"
+            ],
+            "version": "==2.2.5"
+        },
         "atomicwrites": {
             "hashes": [
                 "sha256:03472c30eb2c5d1ba9227e4c2ca66ab8287fbfbbda3888aa93dc2e28fc6811b4",
@@ -486,10 +493,10 @@
         },
         "faker": {
             "hashes": [
-                "sha256:1d3f700e8dfcefd6e657118d71405d53e86974448aba78884f119bbd84c0cddf",
-                "sha256:d5366e120191c5610fceeebfe1c298dc46da0277096f639c6dd7e2eaee0fa547"
+                "sha256:45cc9cca3de8beba5a2da3bd82a6e5544f53da1a702645c8485f682366c15026",
+                "sha256:a6459ff518d1fc6ee2238a7209e6c899517872c7e1115510279033ffe6fe8ef3"
             ],
-            "version": "==2.0.1"
+            "version": "==2.0.2"
         },
         "flake8": {
             "hashes": [
@@ -501,11 +508,11 @@
         },
         "importlib-metadata": {
             "hashes": [
-                "sha256:9ff1b1c5a354142de080b8a4e9803e5d0d59283c93aed808617c787d16768375",
-                "sha256:b7143592e374e50584564794fcb8aaf00a23025f9db866627f89a21491847a8d"
+                "sha256:aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26",
+                "sha256:d5f18a79777f3aa179c145737780282e27b508fc8fd688cb17c7a813e8bd39af"
             ],
             "index": "pypi",
-            "version": "==0.20"
+            "version": "==0.23"
         },
         "inflection": {
             "hashes": [
@@ -542,6 +549,13 @@
             ],
             "version": "==7.5.1"
         },
+        "isort": {
+            "hashes": [
+                "sha256:54da7e92468955c4fceacd0c86bd0ec997b0e1ee80d97f67c35a78b719dccab1",
+                "sha256:6e811fcb295968434526407adb8796944f1988c5b65e8139058f2014cbe100fd"
+            ],
+            "version": "==4.3.21"
+        },
         "jedi": {
             "hashes": [
                 "sha256:786b6c3d80e2f06fd77162a07fed81b8baa22dde5d62896a790a331d6ac21a27",
@@ -574,10 +588,10 @@
         },
         "jupyter-client": {
             "hashes": [
-                "sha256:73a809a2964afa07adcc1521537fddb58c2ffbb7e84d53dc5901cf80480465b3",
-                "sha256:98e8af5edff5d24e4d31e73bc21043130ae9d955a91aa93fc0bc3b1d0f7b5880"
+                "sha256:6a6d415c62179728f6d9295b37356d8f6833e9e01c2b6e1901dc555571f57b21",
+                "sha256:f406f214f9daa92be110d5b83d62f3451ffc73d3522db7350f0554683533ab18"
             ],
-            "version": "==5.3.1"
+            "version": "==5.3.3"
         },
         "jupyter-console": {
             "hashes": [
@@ -627,6 +641,29 @@
             "index": "pypi",
             "version": "==1.1.0"
         },
+        "lazy-object-proxy": {
+            "hashes": [
+                "sha256:02b260c8deb80db09325b99edf62ae344ce9bc64d68b7a634410b8e9a568edbf",
+                "sha256:18f9c401083a4ba6e162355873f906315332ea7035803d0fd8166051e3d402e3",
+                "sha256:1f2c6209a8917c525c1e2b55a716135ca4658a3042b5122d4e3413a4030c26ce",
+                "sha256:2f06d97f0ca0f414f6b707c974aaf8829c2292c1c497642f63824119d770226f",
+                "sha256:616c94f8176808f4018b39f9638080ed86f96b55370b5a9463b2ee5c926f6c5f",
+                "sha256:63b91e30ef47ef68a30f0c3c278fbfe9822319c15f34b7538a829515b84ca2a0",
+                "sha256:77b454f03860b844f758c5d5c6e5f18d27de899a3db367f4af06bec2e6013a8e",
+                "sha256:83fe27ba321e4cfac466178606147d3c0aa18e8087507caec78ed5a966a64905",
+                "sha256:84742532d39f72df959d237912344d8a1764c2d03fe58beba96a87bfa11a76d8",
+                "sha256:874ebf3caaf55a020aeb08acead813baf5a305927a71ce88c9377970fe7ad3c2",
+                "sha256:9f5caf2c7436d44f3cec97c2fa7791f8a675170badbfa86e1992ca1b84c37009",
+                "sha256:a0c8758d01fcdfe7ae8e4b4017b13552efa7f1197dd7358dc9da0576f9d0328a",
+                "sha256:a4def978d9d28cda2d960c279318d46b327632686d82b4917516c36d4c274512",
+                "sha256:ad4f4be843dace866af5fc142509e9b9817ca0c59342fdb176ab6ad552c927f5",
+                "sha256:ae33dd198f772f714420c5ab698ff05ff900150486c648d29951e9c70694338e",
+                "sha256:b4a2b782b8a8c5522ad35c93e04d60e2ba7f7dcb9271ec8e8c3e08239be6c7b4",
+                "sha256:c462eb33f6abca3b34cdedbe84d761f31a60b814e173b98ede3c81bb48967c4f",
+                "sha256:fd135b8d35dfdcdb984828c84d695937e58cc5f49e1c854eb311c4d6aa03f4f1"
+            ],
+            "version": "==1.4.2"
+        },
         "markupsafe": {
             "hashes": [
                 "sha256:00bc623926325b26bb9605ae9eae8a215691f33cae5df11ca5424f06f2d1f473",
@@ -742,11 +779,11 @@
         },
         "pluggy": {
             "hashes": [
-                "sha256:0825a152ac059776623854c1543d65a4ad408eb3d33ee114dff91e57ec6ae6fc",
-                "sha256:b9817417e95936bf75d85d3f8767f7df6cdde751fc40aed3bb3074cbcb77757c"
+                "sha256:0db4b7601aae1d35b4a033282da476845aa19185c1e6964b25cf324b5e4ec3e6",
+                "sha256:fa5fa1622fa6dd5c030e9cad086fa19ef6a0cf6d7a2d12318e10cb49d6d68f34"
             ],
             "index": "pypi",
-            "version": "==0.12.0"
+            "version": "==0.13.0"
         },
         "prometheus-client": {
             "hashes": [
@@ -801,6 +838,14 @@
             ],
             "version": "==2.4.2"
         },
+        "pylint": {
+            "hashes": [
+                "sha256:5d77031694a5fb97ea95e828c8d10fc770a1df6eb3906067aaed42201a8a6a09",
+                "sha256:723e3db49555abaf9bf79dc474c6b9e2935ad82230b10c1138a71ea41ac0fff1"
+            ],
+            "index": "pypi",
+            "version": "==2.3.1"
+        },
         "pyparsing": {
             "hashes": [
                 "sha256:6f98a7b9397e206d78cc01df10131398f1c8b8510a2f4d97d9abd82e1aacdd80",
@@ -945,6 +990,27 @@
             ],
             "version": "==4.3.2"
         },
+        "typed-ast": {
+            "hashes": [
+                "sha256:18511a0b3e7922276346bcb47e2ef9f38fb90fd31cb9223eed42c85d1312344e",
+                "sha256:262c247a82d005e43b5b7f69aff746370538e176131c32dda9cb0f324d27141e",
+                "sha256:2b907eb046d049bcd9892e3076c7a6456c93a25bebfe554e931620c90e6a25b0",
+                "sha256:354c16e5babd09f5cb0ee000d54cfa38401d8b8891eefa878ac772f827181a3c",
+                "sha256:4e0b70c6fc4d010f8107726af5fd37921b666f5b31d9331f0bd24ad9a088e631",
+                "sha256:630968c5cdee51a11c05a30453f8cd65e0cc1d2ad0d9192819df9978984529f4",
+                "sha256:66480f95b8167c9c5c5c87f32cf437d585937970f3fc24386f313a4c97b44e34",
+                "sha256:71211d26ffd12d63a83e079ff258ac9d56a1376a25bc80b1cdcdf601b855b90b",
+                "sha256:95bd11af7eafc16e829af2d3df510cecfd4387f6453355188342c3e79a2ec87a",
+                "sha256:bc6c7d3fa1325a0c6613512a093bc2a2a15aeec350451cbdf9e1d4bffe3e3233",
+                "sha256:cc34a6f5b426748a507dd5d1de4c1978f2eb5626d51326e43280941206c209e1",
+                "sha256:d755f03c1e4a51e9b24d899561fec4ccaf51f210d52abdf8c07ee2849b212a36",
+                "sha256:d7c45933b1bdfaf9f36c579671fec15d25b06c8398f113dab64c18ed1adda01d",
+                "sha256:d896919306dd0aa22d0132f62a1b78d11aaf4c9fc5b3410d3c666b818191630a",
+                "sha256:ffde2fbfad571af120fcbfbbc61c72469e72f550d676c3342492a9dfdefb8f12"
+            ],
+            "markers": "implementation_name == 'cpython'",
+            "version": "==1.4.0"
+        },
         "wcwidth": {
             "hashes": [
                 "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e",
@@ -967,6 +1033,12 @@
             ],
             "version": "==3.5.1"
         },
+        "wrapt": {
+            "hashes": [
+                "sha256:565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1"
+            ],
+            "version": "==1.11.2"
+        },
         "zipp": {
             "hashes": [
                 "sha256:3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e",

backend/metagenedb/apps/catalog/factory/__init__.py

 from .function import FunctionFactory  # noqa
+from .gene import GeneFactory  # noqa
 from .taxonomy import TaxonomyFactory  # noqa

backend/metagenedb/apps/catalog/factory/gene.py

+from factory import DjangoModelFactory, lazy_attribute
+from faker import Factory
+
+from metagenedb.apps.catalog import models
+
+faker = Factory.create()
+
+SELECTED_SOURCE = [i[0] for i in models.Function.SOURCE_CHOICES]
+
+
+class GeneFactory(DjangoModelFactory):
+    class Meta:
+        model = models.Gene
+
+    @lazy_attribute
+    def gene_id(self):
+        return str(faker.pyint())
+
+    @lazy_attribute
+    def length(self):
+        return str(faker.pyint())

backend/metagenedb/apps/catalog/migrations/0010_genefunction.py

+# Generated by Django 2.2.5 on 2019-09-12 13:08
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+from metagenedb.common.utils.chunks import generate_chunks
+
+
+def copy_gene_functions(apps, schema_editor):
+    Gene = apps.get_model('catalog', 'Gene')
+    GeneFunction = apps.get_model('catalog', 'GeneFunction')
+    OldGeneFunctions = Gene.functions.through
+    for chunk in generate_chunks(OldGeneFunctions.objects.all(), 500):
+        new_objs = [GeneFunction(gene=item.gene, function=item.function) for item in chunk]
+        GeneFunction.objects.bulk_create(new_objs)
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('catalog', '0009_meta_unique'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='GeneFunction',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('function', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catalog.Function')),
+                ('gene', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catalog.Gene')),
+            ],
+            options={
+                'unique_together': {('gene', 'function')},
+            },
+        ),
+        migrations.RunPython(copy_gene_functions)
+    ]

backend/metagenedb/apps/catalog/migrations/0011_change_through_genefunction.py

+# Generated by Django 2.2.5 on 2019-09-12 13:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('catalog', '0010_genefunction'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='gene',
+            name='functions',
+            field=models.ManyToManyField(to='catalog.Function'),
+        ),
+        migrations.AddField(
+            model_name='gene',
+            name='functions',
+            field=models.ManyToManyField(through='catalog.GeneFunction', to='catalog.Function'),
+        ),
+    ]

backend/metagenedb/apps/catalog/models/__init__.py

 from .function import Function, KeggOrthology  # noqa
-from .gene import Gene  # noqa
+from .gene import Gene, GeneFunction  # noqa
 from .taxonomy import Taxonomy  # noqa

backend/metagenedb/apps/catalog/models/gene.py

@@ -7,7 +7,7 @@ class Gene(models.Model):
     gene_name = models.CharField(max_length=100, unique=True)
     gene_id = models.SlugField(max_length=100, db_index=True, unique=True)
     length = models.PositiveIntegerField()
-    functions = models.ManyToManyField(Function)
+    functions = models.ManyToManyField(Function, through='GeneFunction')
     taxonomy = models.ForeignKey(
         'Taxonomy', related_name='genes',
         on_delete=models.SET_NULL,
@@ -19,3 +19,16 @@ class Gene(models.Model):
 
     class Meta:
         ordering = ['-gene_id']
+
+
+class GeneFunction(models.Model):
+    gene = models.ForeignKey(Gene, on_delete=models.CASCADE)
+    function = models.ForeignKey(Function, on_delete=models.CASCADE)
+
+    def __str__(self):
+        return f"{self.gene.gene_id} <-> {self.function.function_id}"
+
+    class Meta:
+        unique_together = [
+            'gene', 'function'
+        ]

backend/metagenedb/apps/catalog/serializers/bulk_list.py

+from collections import defaultdict
+
 from rest_framework import serializers
-from rest_framework.exceptions import ValidationError
+from rest_framework.exceptions import ValidationError, ErrorDetail
 from rest_framework.fields import SkipField
 from rest_framework.settings import api_settings
 from rest_framework.utils import html, model_meta
@@ -7,13 +9,20 @@ from rest_framework.utils import html, model_meta
 
 class BulkListSerializer(serializers.ListSerializer):
 
-    def _extract_many_to_many(self, validated_data, info):
-        many_to_many = [{} for v in validated_data]
+    def _extract_many_to_many(self, validated_data, info, lookup_field):
+        many_to_many = {
+            'keys': set(),
+            'values': defaultdict(list)
+        }
         for field_name, relation_info in info.relations.items():
             if relation_info.to_many:
-                for data_item, many_to_many_item in zip(validated_data, many_to_many):
+                for data_item in validated_data:
                     if field_name in data_item:
-                        many_to_many_item[field_name] = data_item.pop(field_name)
+                        many_to_many['keys'].add(field_name)
+                        many_to_many['values'][field_name].append({
+                            field_name: data_item.pop(field_name),
+                            lookup_field: data_item[lookup_field]
+                        })
         return many_to_many
 
     def _get_db_index_fields(self, info):
@@ -68,6 +77,7 @@ class BulkListSerializer(serializers.ListSerializer):
 
         ret = []
         errors = []
+        primary_keys = set()
         for item in data:
             try:
                 if isinstance(self.instance, dict):
@@ -75,6 +85,10 @@ class BulkListSerializer(serializers.ListSerializer):
                     validated = self.child.run_validation(item)
                 else:
                     validated = self.child.run_validation(item)
+                if item[lookup_field] not in primary_keys:
+                    primary_keys.add(item[lookup_field])
+                else:
+                    errors.append(ErrorDetail(item[lookup_field], code='duplicate'))
             except ValidationError as exc:
                 errors.append(exc.detail)
             else:
@@ -88,9 +102,15 @@ class BulkListSerializer(serializers.ListSerializer):
 
     def create(self, validated_data):
         ModelClass = self.Meta.model
+        info = model_meta.get_field_info(ModelClass)
+        lookup_field = self._get_db_index_fields(info)[0]
+        many_to_many = self._extract_many_to_many(validated_data, info, lookup_field)
         instances = ModelClass.objects.bulk_create(
             [ModelClass(**item) for item in validated_data]
         )
+        if many_to_many:
+            for field in many_to_many['keys']:
+                getattr(self, f'_handle_{field}', None)(many_to_many['values'][field])
         return instances
 
     def update(self, instances, validated_data):
@@ -100,8 +120,8 @@ class BulkListSerializer(serializers.ListSerializer):
         """
         ModelClass = self.Meta.model
         info = model_meta.get_field_info(ModelClass)
-        db_index_fields = self._get_db_index_fields(info)
-        lookup_field = db_index_fields[0]
+        lookup_field = self._get_db_index_fields(info)[0]
+        many_to_many = self._extract_many_to_many(validated_data, info, lookup_field)
         updated_keys = self._get_all_key_fields(validated_data)
         validated_data = {item.pop(lookup_field): item for item in validated_data}
         for item_id, validated_data_element in validated_data.items():
@@ -111,6 +131,10 @@ class BulkListSerializer(serializers.ListSerializer):
             list(instances.values()),
             updated_keys
         )
+        # Link existing many-to-many relationships.
+        if many_to_many:
+            for field in many_to_many['keys']:
+                getattr(self, f'_handle_{field}', None)(many_to_many['values'][field])
         return list(instances.values())
 
     class Meta:

backend/metagenedb/apps/catalog/serializers/gene.py

@@ -3,8 +3,7 @@ import traceback
 
 from rest_framework import serializers
 from rest_framework.utils import model_meta
-from metagenedb.apps.catalog.models import Function, Gene, Taxonomy
-from metagenedb.apps.catalog.serializers import FunctionSerializer
+from metagenedb.apps.catalog.models import Function, Gene, GeneFunction, Taxonomy
 
 from .bulk_list import BulkListSerializer
 
@@ -16,11 +15,45 @@ class GeneListSerializer(BulkListSerializer):
     class Meta:
         model = Gene
 
+    def _generate_gene_function_mapping(self, values, genes):
+        """
+        Generate a list of GeneFunction pair to create relation between them
+        """
+        genes_dict = {gene.gene_id: gene for gene in genes}
+        mapping = []
+        for value in values:
+            for function in value['functions']:
+                mapping.append(GeneFunction(gene=genes_dict[value['gene_id']],
+                                            function=function))
+        return mapping
+
+    def _handle_functions(self, values):
+        """
+        :param values: each dictionnary has the 'functions' and 'gene_id' keys
+        :type values: LIST of DICT
+        """
+        # Get all Gene objects
+        gene_ids = [item['gene_id'] for item in values]
+        # Get all link with corresponding genes & Delete them
+        genes = Gene.objects.filter(gene_id__in=gene_ids)
+        GeneFunction.objects.filter(gene__in=genes).delete()
+        # Generate table for bulk_create of function <-> gene and create it
+        GeneFunction.objects.bulk_create(
+            self._generate_gene_function_mapping(values, genes)
+        )
+        print("hi")
+
+    def create(self, validated_data):
+        instances = super().create(validated_data)
+        return instances
+
 
 class GeneSerializer(serializers.ModelSerializer):
-    functions = FunctionSerializer(
+    functions = serializers.SlugRelatedField(
+        queryset=Function.objects.all(),
+        slug_field='function_id',
         many=True,
-        required=False
+        required=False,
     )
     taxonomy = serializers.SlugRelatedField(
         queryset=Taxonomy.objects.all(),
@@ -43,12 +76,12 @@ class GeneSerializer(serializers.ModelSerializer):
     def _handle_functions(self, functions, instance):
         for function in functions:
             try:
-                function = Function.objects.get(function_id=function.get('function_id'))
+                function = Function.objects.get(function_id=function)
                 instance.functions.add(function)
                 instance.full_clean()
                 instance.save()
             except Function.DoesNotExist:
-                _LOGGER.warning(f"{function.get('function_id')} not found for {instance.gene_id}. Function ignored")
+                _LOGGER.warning("%s not found for %s. Function ignored", function, instance.gene_id)
 
     def create(self, validated_data):
         ModelClass = self.Meta.model

backend/metagenedb/apps/catalog/serializers/test_bulk_list.py

@@ -3,6 +3,7 @@ from unittest import TestCase
 from unittest.mock import Mock
 
 from rest_framework.test import APITestCase
+from rest_framework.exceptions import ValidationError
 
 from metagenedb.apps.catalog.serializers import FunctionSerializer
 from metagenedb.apps.catalog.serializers.bulk_list import BulkListSerializer
@@ -23,8 +24,8 @@ class BaseTestBulkListSerializerMethods(TestCase):
 
     def setUp(self):
         self.data = [
-            {'field1': 'value1', 'field2': 'value2'},
-            {'field1': 'value3', 'field2': 'value4'}
+            {'id': 'entry_1', 'field1': 'value1', 'field2': 'value2'},
+            {'id': 'entry_2', 'field1': 'value3', 'field2': 'value4'}
         ]
         self.bulk_list_serializer = BulkListSerializerTestExtractManyToMany()
         self.info = Mock()
@@ -38,12 +39,40 @@ class TestExtractManyToMany(BaseTestBulkListSerializerMethods):
             'field2': Mock(to_many=False)
         }
         ori_list = deepcopy(self.data)
-        expected_list = [
-            {'field1': 'value1'},
-            {'field1': 'value3'}
-        ]
-        tested_list = self.bulk_list_serializer._extract_many_to_many(self.data, self.info)
-        self.assertListEqual(tested_list, expected_list)
+        expected_dict = {
+            'keys': {'field1'},
+            'values': {
+                'field1': [
+                    {'field1': 'value1', 'id': 'entry_1'},
+                    {'field1': 'value3', 'id': 'entry_2'}
+                ]
+            }
+        }