Merge pull request #118 from ProteinsWebTeam/dev

Release 97.0

config/interpro.yml

@@ -37,7 +37,7 @@ members:
   panther:
     filter: "panther"
     label: "PANTHER"
-    accession: 'PTHR[0-9]{5}(:SF[0-9]{1,3})?$'
+    accession: 'PTHR[0-9]{5}(:SF[0-9]{1,4})?$'
     options: []
     options_per_family: []
   pirsf:

interpro/urls.py

@@ -2,6 +2,6 @@
 from webfront.views import common, mail
 
 urlpatterns = [
-    url(r"^api/mail/$", mail.mail_interhelp),
+    url(r"^api/mail/$", mail.send_email),
     url(r"^api/(?P<url>.*)$", common.GeneralHandler.as_view()),
 ]

webfront/exceptions.py

@@ -1,9 +1,12 @@
 class DeletedEntryError(Exception):
-    def __init__(self, accession, date, message, history):
+    def __init__(self, accession, database, _type, name, short_name, history, date):
         self.accession = accession
-        self.message = message
-        self.date = date
+        self.database = database
+        self.type = _type
+        self.name = name
+        self.short_name = short_name
         self.history = history
+        self.date = date
 
 
 class EmptyQuerysetError(Exception):

webfront/migrations/0023_rename_is_alive_entry_is_public.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.20 on 2023-09-19 21:37
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('webfront', '0022_chain_sequence'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='entry',
+            old_name='is_alive',
+            new_name='is_public',
+        ),
+    ]

webfront/migrations/0024_entry_llm_description.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.19 on 2023-10-03 11:38
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('webfront', '0023_rename_is_alive_entry_is_public'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='entry',
+            name='llm_description',
+            field=models.TextField(null=True),
+        ),
+    ]

webfront/models/interpro_new.py

@@ -31,14 +31,15 @@ class Entry(models.Model):
     )
     go_terms = JSONField(null=True)
     description = JSONField(null=True)
+    llm_description = models.TextField(null=True)
     wikipedia = JSONField(null=True)
     literature = JSONField(null=True)
     hierarchy = JSONField(null=True)
     cross_references = JSONField(null=True)
     entry_date = models.DateTimeField(null=True)
     is_featured = models.BooleanField(default=False)
     overlaps_with = JSONField(default=[])
-    is_alive = models.BooleanField(default=False)
+    is_public = models.BooleanField(default=False)
     deletion_date = models.DateTimeField(null=True)
     counts = JSONField(null=True)
     interactions = JSONField(null=True)

webfront/serializers/interpro.py

@@ -230,6 +230,7 @@ def to_metadata_representation(instance, searcher, sq, counters=None):
                 # "other": instance.other_names,
             },
             "description": instance.description,
+            "llm_description": instance.llm_description,
             "wikipedia": instance.wikipedia,
             "literature": instance.literature,
             "set_info": instance.set_info,

webfront/tests/fixtures_entry.json

@@ -10,7 +10,7 @@
       "source_database": "interpro",
       "entry_date": "2001-04-21T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "member_databases": {
         "smart": {
           "SM00950": "Piwi domain"
@@ -173,7 +173,7 @@
       "member_databases": {},
       "entry_date": "2002-04-21T00:00:00Z",
       "is_featured": false,
-      "is_alive": true,
+      "is_public": true,
       "integrated": null,
       "hierarchy": {
         "children": [
@@ -284,7 +284,7 @@
       "type": "domain",
       "name": "Piwi domain",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "entry_date": "2003-04-21T00:00:00Z",
       "short_name": "Piwi",
       "go_terms": [
@@ -392,7 +392,7 @@
       "name": "Piwi domain",
       "entry_date": "2004-04-21T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "short_name": "Piwi",
       "go_terms": [
         {
@@ -432,7 +432,7 @@
       "entry_date": "2001-04-21T00:00:00Z",
       "name": "PIWI",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "short_name": "Piwi",
       "go_terms": [],
       "source_database": "profile",
@@ -461,7 +461,7 @@
       "entry_id": "id3",
       "type": "domain",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "entry_date": "2002-04-21T00:00:00Z",
       "go_terms": [],
       "source_database": "pfam",
@@ -491,7 +491,7 @@
       "type": "domain",
       "entry_date": "2002-04-21T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "go_terms": [],
       "source_database": "pfam",
       "member_databases": {},
@@ -521,7 +521,7 @@
       "name": "Myelin family",
       "entry_date": "2003-04-21T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "short_name": "Myelin",
       "go_terms": [
         {
@@ -563,7 +563,7 @@
       "go_terms": [],
       "entry_date": "2004-04-21T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "source_database": "profile",
       "member_databases": null,
       "integrated": null,
@@ -594,7 +594,7 @@
       "go_terms": [],
       "entry_date": "2014-04-21T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "source_database": "ncbifam",
       "member_databases": null,
       "integrated": null,
@@ -616,12 +616,13 @@
     "model": "webfront.Entry",
     "fields": {
       "entry_id": null,
-      "accession": "IPR123456",
-      "type": "D",
-      "name": "Deleted",
-      "entry_date": "1994-04-21T00:00:00Z",
-      "deletion_date": "1994-04-21T00:00:00Z",
-      "is_alive": false,
+      "accession": "IPR000005",
+      "type": "domain",
+      "name": "HTH transcriptional regulator, AraC",
+      "short_name": "HTH_AraC",
+      "entry_date": "1999-10-08T17:07:25Z",
+      "deletion_date": "2010-10-28T10:51:29Z",
+      "is_public": true,
       "source_database": "interpro",
       "history": {
         "names": [
@@ -630,32 +631,45 @@
           "Helix-turn-helix, AraC type",
           "HTH transcriptional regulator, AraC"
         ],
-        "signatures": [
-          {
-            "accession": "PS00041",
-            "exists": true,
-            "integrated_id": "IPR018062"
+        "short_names": [
+          "HTHAraC",
+          "HTH_AraC-typ",
+          "HTH_AraC"
+        ],
+        "signatures": {
+          "prosite": {
+            "PS00041": "IPR018062"
           },
-          {
-            "accession": "PR00032",
-            "exists": true,
-            "integrated_id": "IPR020449"
+          "pfam": {
+            "PF00165": "IPR018060"
           },
-          {
-            "accession": "PF00165",
-            "exists": true,
-            "integrated_id": "IPR018060"
+          "prints": {
+            "PR00032": "IPR020449"
           },
-          {
-            "accession": "PS01124",
-            "exists": true,
-            "integrated_id": "IPR018060"
+          "profile": {
+            "PS01124": "IPR018060"
           },
-          {
-            "accession": "SM00342",
-            "exists": true,
-            "integrated_id": "IPR018060"
+          "smart": {
+            "SM00342": "IPR018060"
           }
+        }
+      }
+    }
+  },
+  {
+    "model": "webfront.Entry",
+    "fields": {
+      "entry_id": null,
+      "accession": "PF20534",
+      "type": "domain",
+      "short_name": "DUF6749",
+      "entry_date": "2022-07-01T14:20:35Z",
+      "deletion_date": "2023-07-24T17:42:21Z",
+      "is_public": true,
+      "source_database": "pfam",
+      "history": {
+        "short_names": [
+          "DUF6749"
         ]
       }
     }
@@ -671,7 +685,7 @@
       "go_terms": [],
       "entry_date": "2014-03-02T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "source_database": "panther",
       "member_databases": null,
       "integrated": null,
@@ -703,7 +717,7 @@
       "go_terms": [],
       "entry_date": "2014-03-02T00:00:00Z",
       "is_featured": true,
-      "is_alive": false,
+      "is_public": false,
       "source_database": "panther",
       "member_databases": null,
       "integrated": "PTHR43214",
@@ -733,7 +747,7 @@
       "go_terms": [],
       "entry_date": "2004-03-02T00:00:00Z",
       "is_featured": true,
-      "is_alive": true,
+      "is_public": true,
       "source_database": "cathgene3d",
       "member_databases": null,
       "integrated": null,
@@ -763,7 +777,7 @@
       "go_terms": [],
       "entry_date": "2004-03-02T00:00:00Z",
       "is_featured": true,
-      "is_alive": false,
+      "is_public": false,
       "source_database": "cathgene3d",
       "member_databases": null,
       "integrated": "G3DSA:1.10.10.10",
@@ -780,5 +794,35 @@
         "domain_architectures": 0
       }
     }
+  },
+  {
+    "model": "webfront.Entry",
+    "fields": {
+      "entry_id": null,
+      "accession": "PTHR10000",
+      "type": "family",
+      "name": "PHOSPHOSERINE PHOSPHATASE",
+      "source_database": "panther",
+      "llm_description": "<p>The protein family belongs to the HAD-like hydrolase superfamily and includes subfamilies such as the Cof family, CbbY/CbbZ/Gph/YieH family, SupH subfamily, the archaeal SPP-like hydrolase family, and the MPGP family. The proteins in this family function as phosphatases, catalyzing the dephosphorylation of various substrates. These include 2-phosphoglycolate, the riboflavin precursor 5-amino-6-(5-phospho-D-ribitylamino)uracil, flavin mononucleotide (FMN), pyridoxal-phosphate (PLP), and different sugar phosphates. Some proteins specifically hydrolyze mannosyl-3-phosphoglycerate (MPG) to form the osmolyte mannosylglycerate (MG), while others are involved in the biosynthesis of kanosamine and glucosylglycerate. The activity of these proteins can be inhibited by high concentrations of Ca(2+) ions and chloride ions.</p>",
+      "is_featured": false,
+      "is_public": true,
+      "entry_date": "2005-09-11T00:00:00Z",
+      "counts": {
+        "subfamilies": 8,
+        "domain_architectures": 0,
+        "interactions": 0,
+        "matches": 91777,
+        "pathways": 0,
+        "proteins": 91777,
+        "proteomes": 6899,
+        "sets": 0,
+        "structural_models": {
+          "alphafold": 79631,
+          "rosettafold": 0
+        },
+        "structures": 36,
+        "taxa": 28523
+      }
+    }
   }
 ]

webfront/tests/test_mail.py

@@ -1,9 +1,12 @@
+import time
+
 from django.test import TestCase
 from django.test import Client
+from rest_framework import status
 
 
 class TestMail(TestCase):
-    def test_mail(self):
+    def test_mail(self, sleep=60):
         self.client = Client()
         response = self.client.post(
             "/api/mail/",
@@ -14,4 +17,37 @@ def test_mail(self):
                 "from_email": "swaathik@ebi.ac.uk",
             },
         )
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
         self.assertEqual(response.json()["from"], "swaathik@ebi.ac.uk")
+        time.sleep(sleep)
+
+    def test_spam(self):
+        self.test_mail(sleep=0)
+        self.client = Client()
+        response = self.client.post(
+            "/api/mail/",
+            {
+                "path": "echo",
+                "subject": "Add annotation test from API",
+                "message": "Test",
+                "from_email": "swaathik@ebi.ac.uk",
+            },
+        )
+        self.assertEqual(response.status_code,
+                         status.HTTP_429_TOO_MANY_REQUESTS)
+        time.sleep(60)
+
+    def test_mail_invalid_queue(self):
+        self.client = Client()
+        response = self.client.post(
+            "/api/mail/",
+            {
+                "path": "echo",
+                "subject": "Add annotation test from API",
+                "message": "Test",
+                "queue": "uniprot",
+                "from_email": "swaathik@ebi.ac.uk",
+            },
+        )
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+        time.sleep(60)