Merge branch 'main' into dev

Author: erikhuck

.github/workflows/build_documentation.yml

@@ -11,13 +11,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    # Standard drop-in approach that should work for most people.
-    - uses: ammaraskar/sphinx-action@master
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
       with:
-        docs-folder: "docs/"
+        python-version: '3.11'
+    - name: Upgrade pip, install package, install requirements, build docs
+      run: |
+        pip install --upgrade pip
+        pip install -r ./docs/requirements.txt
+        sphinx-build docs ./docs/_build/html/
     # Create an artifact of the html output.
-    - uses: actions/upload-artifact@v1
+    - uses: actions/upload-artifact@v3
       with:
         name: DocumentationHTML
         path: docs/_build/html/

dev/test_data/all-brite-entry-ids.txt

@@ -89,9 +89,9 @@ br:br08310
 br:br08307
 br:br08327
 br:br08311
+br:br08403
 br:br08402
 br:br08401
-br:br08403
 br:br08411
 br:br08410
 br:br08420

dev/test_data/brite-entries/br_br08902.txt

@@ -96,7 +96,6 @@ B  Drug classifications
 C    br08303  Anatomical Therapeutic Chemical (ATC) classification
 C    br08302  USP drug classification
 C    br08301  Therapeutic category of drugs in Japan
-C    br08303_ndc  Anatomical Therapeutic Chemical (ATC) classification + Product (NDC)
 C    br08313  Classification of Japanese OTC drugs
 C    br08312  Risk category of Japanese OTC drugs
 C    br08304  Traditional Chinese Medicine in Japan
@@ -111,11 +110,9 @@ C    br08327  Antimicrobials abbreviations
 C    br08311  Drugs listed in the Japanese Pharmacopoeia
 ADiseases
 B  Human diseases
-C    br08402  Human diseases
-C    br08401  Infectious diseases
-C    br08402_gene  Human diseases + Genes
-C    br08401_genome  Infectious diseases + Genomes
 C    br08403  Human diseases in ICD-11 classification
+C    br08402  Pathway-based classification of diseases
+C    br08401  Genome-based classification of infectious diseases
 C    br08411  ICD-11 International Classification of Diseases
 C    br08410  ICD-10 International Classification of Diseases
 C    br08420  ICD-O-3 International Classification of Diseases for Oncology
@@ -134,5 +131,5 @@ B  Organism information
 C    br08605  Plant pathogens
 !
 #
-#Last updated: April 4, 2023
+#Last updated: June 1, 2023
 #» Japanese version

dev/test_data/drug-entry-ids.txt

@@ -395,4 +395,5 @@ dr:D12390
 dr:D12391
 dr:D12423
 dr:D12467
-dr:D12559
+dr:D12559
+dr:D12604