add ncbi key (#231)

Author: tlambert03

.github/workflows/ci.yml

@@ -36,6 +36,7 @@ jobs:
       # postgres://user:password@host:port/database
       DATABASE_URL: "postgres://postgres:postgres@localhost:5432/postgres"
       UV_FROZEN: 1
+      NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
     steps:
       - name: Checkout Code Repository
         uses: actions/checkout@v4

backend/references/helpers.py

@@ -1,13 +1,15 @@
 import contextlib
 import datetime
 import json
+import os
 import re
 
 import requests
 from Bio import Entrez
 from habanero import Crossref
 
 Entrez.email = "[email protected]"
+Entrez.api_key = os.getenv("NCBI_API_KEY", None)
 email = Entrez.email
 ID_CONVERT_URL = (
     "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?tool=FPbase&email=" + email + "&ids=%s&format=json"

pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
     'drf-spectacular==0.26.3',
     'djangorestframework-csv==2.1.1',
     'django-recaptcha==3.0.0',
-    'sentry-sdk==1.31.0',
+    'sentry-sdk>=2.8',
     'biopython==1.83',
     'pandas==2.0.3',
     'parasail==1.3.4',
@@ -34,7 +34,7 @@ dependencies = [
     'django-reversion-compare==0.16.2',
     'tablib==3.4.0',
     'scipy==1.14.1',
-    'dnspython==2.3.0',
+    'dnspython>=2.6.1',
     'django-anymail==10.0',
     'django-autocomplete-light==3.11.0',
     'django-avatar==7.1.1',

requirements.txt

@@ -344,9 +344,9 @@ djangorestframework==3.14.0 \
     --hash=sha256:eb63f58c9f218e1a7d064d17a70751f528ed4e1d35547fdade9aaf4cd103fd08
 djangorestframework-csv==2.1.1 \
     --hash=sha256:aa0ee4c894fe319c68e042b05c61dace43a9fb6e6872e1abe1724ca7ea4d15f7
-dnspython==2.3.0 \
-    --hash=sha256:224e32b03eb46be70e12ef6d64e0be123a64e621ab4c0822ff6d450d52a540b9 \
-    --hash=sha256:89141536394f909066cabd112e3e1a37e4e654db00a25308b0f130bc3152eb46
+dnspython==2.7.0 \
+    --hash=sha256:b4c34b7d10b51bcc3a5071e7b8dee77939f1e878477eeecc965e9835f63c6c86 \
+    --hash=sha256:ce9c432eda0dc91cf618a5cedf1a4e142651196bbcd2c80e89ed5a907e5cfaf1
 drf-spectacular==0.26.3 \
     --hash=sha256:1d84ac70522baaadd6d84a25ce5fe5ea50cfcba0387856689f98ac536f14aa32 \
     --hash=sha256:b907a72a0244e5dcfeca625e9632cd8ebccdbe2cb528b7c1de1191708be6f31e
@@ -826,9 +826,9 @@ scipy==1.14.1 \
     --hash=sha256:eb58ca0abd96911932f688528977858681a59d61a7ce908ffd355957f7025cfc \
     --hash=sha256:edaf02b82cd7639db00dbff629995ef185c8df4c3ffa71a5562a595765a06ce1 \
     --hash=sha256:fef8c87f8abfb884dac04e97824b61299880c43f4ce675dd2cbeadd3c9b466d2
-sentry-sdk==1.31.0 \
-    --hash=sha256:64a7141005fb775b9db298a30de93e3b83e0ddd1232dc6f36eb38aebc1553291 \
-    --hash=sha256:6de2e88304873484207fed836388e422aeff000609b104c802749fd89d56ba5b
+sentry-sdk==2.21.0 \
+    --hash=sha256:7623cfa9e2c8150948a81ca253b8e2bfe4ce0b96ab12f8cd78e3ac9c490fd92f \
+    --hash=sha256:a6d38e0fb35edda191acf80b188ec713c863aaa5ad8d5798decb8671d02077b6
 setuptools==75.8.0 \
     --hash=sha256:c5afc8f407c626b8313a86e10311dd3f661c6cd9c09d4bf8c15c0e11f9f2b0e6 \
     --hash=sha256:e3982f444617239225d675215d51f6ba05f845d4eec313da4418fdbb56fb27e3