Merge pull request #272 from MetaCell/develop

Release 1.6.0

applications/portal/api/openapi.yaml

@@ -403,6 +403,27 @@ paths:
                 -
                     bearerAuth: []
                     cookieAuth: []
+    /partners:
+        description: get the list of partners and related images
+        get:
+            responses:
+                '200':
+                    content:
+                        application/json:
+                            schema:
+                                type: array
+                                items:
+                                    $ref: '#/components/schemas/PartnerResponseObject'
+                            examples:
+                                Partner Response:
+                                    value:
+                                        -
+                                            name: Partner 1
+                                            url: www.partner.com
+                                            image: 'https:areg.com/media/partner/image.jpg'
+                    description: ''
+            operationId: getPartners
+            summary: get the list of partners and related images
 components:
     schemas:
         KeyValuePair:
@@ -833,6 +854,21 @@ components:
                     $ref: '#/components/schemas/AbstractAntibody'
                 -
                     $ref: '#/components/schemas/AntibodyCoreId'
+        PartnerResponseObject:
+            title: Root Type for PartnerResponse
+            description: Response of the list of partners and related images
+            type: object
+            properties:
+                name:
+                    type: string
+                url:
+                    type: string
+                image:
+                    type: string
+            example:
+                name: Partner 1
+                url: www.partner.com
+                image: 'https:areg.com/media/partner/image.jpg'
     responses:
         PaginatedAntibodies:
             content:

applications/portal/backend/.gitignore

@@ -1 +1,2 @@
-antibody_data
+antibody_data
+persistent/partners

applications/portal/backend/api/admin.py

@@ -25,7 +25,8 @@
     Vendor,
     Specie,
     VendorDomain,
-    VendorSynonym, AntibodyFiles, CommercialType
+    VendorSynonym, AntibodyFiles, CommercialType,
+    Partner,
 )
 from api.import_export import AntibodyResource
 from api.services.keycloak_service import KeycloakService
@@ -442,3 +443,8 @@ def get_deleted_objects(self, objs, request):
                 self._force_delete(src_vendor)
                 return super().get_deleted_objects(objs, request)
         return super().get_deleted_objects(objs, request)
+
+
+@admin.register(Partner)
+class PartnerAdmin(admin.ModelAdmin):
+    pass

applications/portal/backend/api/controllers/api_controller.py

@@ -1,6 +1,17 @@
-from openapi.models import DataInfo
-from api.services import antibody_service
+from openapi.models import DataInfo, PartnerResponseObject
+from api.services import antibody_service, partner_service
+from typing import List
+from django.conf import settings
 
 
 def get_datainfo():
     return DataInfo(total=antibody_service.count(), lastupdate=antibody_service.last_update())
+
+def get_partners() -> List[PartnerResponseObject]:
+    return [
+        PartnerResponseObject(
+            name=partner.name,
+            url=partner.url,
+            image=f"{settings.MEDIA_URL}{partner.image}" if partner.image else None
+        ) for partner in partner_service.get_all_partners()
+    ]

applications/portal/backend/api/migrations/0015_add_partner_model.py

@@ -0,0 +1,38 @@
+# Generated by Django 4.2.11 on 2025-01-03 11:05
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("api", "0014_remove_antibodysearch_citations_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="Partner",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("name", models.CharField(db_index=True, max_length=512)),
+                ("url", models.URLField(db_index=True, max_length=2048)),
+                (
+                    "image",
+                    models.ImageField(blank=True, null=True, upload_to="partners"),
+                ),
+            ],
+            options={
+                "verbose_name_plural": "Partners",
+                "ordering": ("name",),
+            },
+        ),
+    ]

applications/portal/backend/api/migrations/0016_auto_20250103_0311.py

@@ -0,0 +1,83 @@
+# Generated by Django 4.2.11 on 2025-01-03 11:11
+
+from django.db import migrations
+from django.core.files import File
+import os
+
+common_file_path_for_partners_image_data = "api/migrations/data/partners"
+
+partners = [
+    {"name": "thermofisher", "url": "https://www.thermofisher.com/", "image": f"{common_file_path_for_partners_image_data}/thermofisher.jpg"},
+    {"name": "proteintech", "url": "https://www.ptglab.com/", "image": f"{common_file_path_for_partners_image_data}/proteintech.jpg"},
+    {"name": "biocell", "url": "https://bxcell.com/", "image": f"{common_file_path_for_partners_image_data}/biocell.jpg"},
+    {"name": "chromotek", "url": "http://www.chromotek.com/home-of-alpaca-antibodies/", "image": f"{common_file_path_for_partners_image_data}/chromotek.jpg"},
+    {"name": "jesselllab", "url": "https://jesselllab.com/", "image": f"{common_file_path_for_partners_image_data}/jesselllab.jpg"},
+    {"name": "encorbio", "url": "https://encorbio.com/", "image": f"{common_file_path_for_partners_image_data}/encorbio.jpg"},
+    {"name": "biolegend", "url": "https://www.biolegend.com/", "image": f"{common_file_path_for_partners_image_data}/biolegend.jpg"},
+    {"name": "leinco", "url": "https://www.leinco.com/", "image": f"{common_file_path_for_partners_image_data}/leinco.jpg"},
+    {"name": "jacksonimmuno", "url": "https://www.jacksonimmuno.com/", "image": f"{common_file_path_for_partners_image_data}/jacksonimmuno.jpg"},
+    {"name": "dshb", "url": "http://dshb.biology.uiowa.edu/", "image": f"{common_file_path_for_partners_image_data}/dshb.jpg"},
+    {"name": "immunostar", "url": "http://immunostar.com/", "image": f"{common_file_path_for_partners_image_data}/immunostar.jpg"},
+    {"name": "neuromab", "url": "http://neuromab.ucdavis.edu/", "image": f"{common_file_path_for_partners_image_data}/neuromab.jpg"},
+    {"name": "sysy", "url": "https://www.sysy.com/", "image": f"{common_file_path_for_partners_image_data}/sysy.jpg"},
+    {"name": "atlasantibodies", "url": "https://atlasantibodies.com/", "image": f"{common_file_path_for_partners_image_data}/atlasantibodies.jpg"},
+    {"name": "frontier", "url": "https://www.frontier-institute.com/wp/antibodies/?lang=en", "image": f"{common_file_path_for_partners_image_data}/frontier.jpg"},
+    {"name": "aeonianbiotech", "url": "https://aeonianbiotech.com/", "image": f"{common_file_path_for_partners_image_data}/aeonianbiotech.jpg"},
+    {"name": "bdbiosciences", "url": "http://www.bdbiosciences.com/us/home", "image": f"{common_file_path_for_partners_image_data}/bdbiosciences.jpg"},
+    {"name": "miltenyibiotec", "url": "https://www.miltenyibiotec.com/US-en/", "image": f"{common_file_path_for_partners_image_data}/miltenyibiotec.jpg"},
+    {"name": "revmab", "url": "https://www.revmab.com/", "image": f"{common_file_path_for_partners_image_data}/revmab.jpg"},
+    {"name": "southernbiotech", "url": "https://www.southernbiotech.com/", "image": f"{common_file_path_for_partners_image_data}/southernbiotech.jpg"},
+    {"name": "wagner", "url": "http://gwagner.med.harvard.edu/", "image": f"{common_file_path_for_partners_image_data}/wagner.jpg"},
+    {"name": "zebrafish", "url": "https://zebrafish.org/home/guide.php", "image": f"{common_file_path_for_partners_image_data}/zebrafish.jpg"},
+    {"name": "genetex", "url": "https://www.genetex.com/", "image": f"{common_file_path_for_partners_image_data}/genetex.jpg"},
+    {"name": "licor", "url": "https://www.licor.com/bio", "image": f"{common_file_path_for_partners_image_data}/LICORbio.png"},
+    {"name": "hytest", "url": "https://www.hytest.fi/home", "image": f"{common_file_path_for_partners_image_data}/hytest.jpg" },
+    {"name": "Ansh Labs", "url": "https://www.anshlabs.com/", "image": f"{common_file_path_for_partners_image_data}/anshlabs.png"},
+    {"name": "Oasis Biofarm", "url": "https://www.oasisbiofarm.net", "image": f"{common_file_path_for_partners_image_data}/oasis.png"},
+    {"name": "Nittobo Medical", "url": "https://www.nittobo.co.jp/", "image": f"{common_file_path_for_partners_image_data}/Nittobo.png"},
+    {"name": "SICGEN", "url": "https://sicgen.pt/", "image": f"{common_file_path_for_partners_image_data}/Sicgen_antibodies.png"},
+    {"name": "Sino Biological", "url": "https://www.sinobiological.com/", "image": f"{common_file_path_for_partners_image_data}/Sino-Biological.png"},
+    {"name": "Niels Danbolt University of Oslo", "url": "https://www.uio.no/", "image": f"{common_file_path_for_partners_image_data}/University_of_Oslo.png"},
+    {"name": "NIH", "url": "https://www.nhpreagents.org/", "image": f"{common_file_path_for_partners_image_data}/NIH.png"},
+    {"name": "ichorbio", "url": "https://ichor.bio/", "image": f"{common_file_path_for_partners_image_data}/ichorbio.png"},
+    {"name": "Antibodies Incorporated", "url": "https://www.antibodiesinc.com/", "image": f"{common_file_path_for_partners_image_data}/antibodies_incorporated.jpg"},
+    {"name": "HUABIO", "url": "https://www.huabio.com/", "image": f"{common_file_path_for_partners_image_data}/HUABIO.png"},
+    {"name": "NanoTag", "url": "https://nano-tag.com/", "image": f"{common_file_path_for_partners_image_data}/NanoTag.jpg"},
+    {"name": "Institute for Protein Innovation", "url": "https://proteininnovation.org/", "image": f"{common_file_path_for_partners_image_data}/Institute_for_Protein_Innovation.png"},
+    {"name": "Fujirebio", "url": "https://www.fujirebio.com/en", "image": f"{common_file_path_for_partners_image_data}/Fujirebio.jpeg"},
+    {"name": "Boster Biological Technology", "url": "https://www.bosterbio.com/", "image": f"{common_file_path_for_partners_image_data}/Boster_Biological-logo.png"},
+    {"name": "Fujifilm Wako USA", "url": "https://wakousa.com/", "image": f"{common_file_path_for_partners_image_data}/fujifilm-wako-chemicals-usa-corporation-logo-vector.png"},
+    {"name": "Active Motif", "url": "https://www.activemotif.com/", "image": f"{common_file_path_for_partners_image_data}/Active-Motif.jpg"},
+    {"name": "Life Canvas Technologies", "url": "https://lifecanvastech.com/", "image": f"{common_file_path_for_partners_image_data}/LifeCanvas.jpeg"},
+    {"name": "AdipoGen Life Sciences", "url": "https://adipogen.com/", "image": f"{common_file_path_for_partners_image_data}/AdipoGen_Logo_LIFE_SCIENCES_CMYK_2015_NEW_13cm_lowres.jpg"},
+    {"name": "Creative Biolabs", "url": "https://www.creativebiolabs.net/?utm_source=antibodyregistry&utm_medium=logo&utm_campaign=Creative+Biolabs-Recombinant+Antibody", "image": f"{common_file_path_for_partners_image_data}/biolabs.png"},
+    {"name": "Bio-techne", "url": "https://www.bio-techne.com/", "image": f"{common_file_path_for_partners_image_data}/bio-techne.png"},
+    {"name": "Bio-Rad", "url": "https://www.bio-rad.com/", "image": f"{common_file_path_for_partners_image_data}/bio-rad.jpg"}
+]
+
+def add_partners(apps, schema_editor):
+    Partner = apps.get_model('api', 'Partner')
+    for partner in partners:
+        if partner.get("image"):
+            image_path = partner["image"]
+            with open(image_path, 'rb') as image_file:
+                Partner.objects.create(
+                    name=partner["name"],
+                    url=partner["url"],
+                    image=File(image_file, name=os.path.basename(image_path))
+                )
+        else:
+            Partner.objects.create(
+                name=partner["name"],
+                url=partner["url"]
+            )
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("api", "0015_add_partner_model"),
+    ]
+
+    operations = [
+        migrations.RunPython(add_partners),
+    ]

applications/portal/backend/api/models.py

@@ -637,3 +637,16 @@ class Meta:
                 name='antibody_search_fts_idx'),
 
         ]
+
+
+class Partner(models.Model):
+    name = models.CharField(max_length=VENDOR_MAX_LEN, db_index=True)
+    url = models.URLField(max_length=URL_MAX_LEN, db_index=True)
+    image = models.ImageField(upload_to='partners', null=True, blank=True)
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        ordering = ('name',)
+        verbose_name_plural = "Partners"

applications/portal/backend/api/services/partner_service.py

@@ -0,0 +1,4 @@
+from api.models import Partner
+
+def get_all_partners():
+	return Partner.objects.all()

applications/portal/backend/main.py

@@ -1,6 +1,6 @@
 # generated by fastapi-codegen:
 #   filename:  openapi.yaml
-#   timestamp: 2024-05-15T15:25:40+00:00
+#   timestamp: 2025-01-03T12:32:56+00:00
 
 from __future__ import annotations
 
@@ -21,6 +21,7 @@
     FilterRequest,
     IngestRequest,
     PaginatedAntibodies,
+    PartnerResponseObject,
     UpdateAntibody,
 )
 from starlette.middleware.cors import CORSMiddleware
@@ -268,7 +269,6 @@ def get_antibody(antibody_id: int) -> List[Antibody]:
 
 @prefix_router.get('/datainfo', response_model=DataInfo, tags=None)
 def get_datainfo() -> DataInfo:
-
     return api_controller.get_datainfo()
 
 
@@ -292,6 +292,15 @@ def live() -> str:
     return test_controller.live()
 
 
+@prefix_router.get('/partners', response_model=List[PartnerResponseObject], tags=None)
+def get_partners() -> List[PartnerResponseObject]:
+    """
+    get the list of partners and related images
+    """
+
+    return api_controller.get_partners()
+
+
 @prefix_router.get('/ping', response_model=str, tags=['test'])
 def ping() -> str:
     """
@@ -318,6 +327,6 @@ def ready() -> str:
 #    import uvicorn
 #    uvicorn.run(app, host="0.0.0.0", port=8000)
 
-from api.helpers import init_sentry # noqa: E402
+from api.helpers import init_sentry  # noqa E402
 
 init_sentry()

applications/portal/backend/openapi/models.py

@@ -301,3 +301,10 @@ class PaginatedAntibodies(BaseModel):
     page: float = Field(..., description='')
     totalElements: int = Field(..., description='')
     items: List[Antibody] = Field(..., description='')
+
+
+class PartnerResponseObject(BaseModel):
+    name: Optional[str] = None
+    url: Optional[str] = None
+    image: Optional[str] = None
+

applications/portal/deploy/values.yaml

@@ -16,6 +16,12 @@ harness:
       limits:
         cpu: 4
         memory: 2Gi
+    volume:
+      name: areg-persistent-files
+      mountpath: /usr/src/app/persistent
+      auto: true
+      size: 5Gi
+      usenfs: false
   livenessProbe:
     path: /api/live
   readinessProbe: