renamed and added algorithm to who

.github/workflows/pr-build-check.yml

@@ -17,8 +17,9 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       herpesdrg: ${{ steps.filter.outputs.herpesdrg }}
-      hsv_daehne_jaki: ${{ steps.filter.outputs.hsv_daehne_jaki }}
+      simplexvirus-db: ${{ steps.filter.outputs.simplexvirus-db }}
       stanford-hiv: ${{ steps.filter.outputs.stanford-hiv }}
+      who-influenza: ${{ steps.filter.outputs.who-influenza }}
       charmd: ${{ steps.filter.outputs.charmd }}
       any: ${{ steps.filter.outputs.any }}
     steps:
@@ -36,15 +37,18 @@ jobs:
               - 'databases/charmd/**'
             herpesdrg:
               - 'databases/herpesdrg/**'
-            hsv_daehne_jaki:
-              - 'databases/hsv_daehne_jaki/**'
+            simplexvirus-db:
+              - 'databases/simplexvirus-db/**'
             stanford-hiv:
               - 'databases/stanford-hiv/**'
+            who-influenza:
+              - 'databases/who-influenza/**'
             any:
               - 'databases/charmd/**'
               - 'databases/herpesdrg/**'
-              - 'databases/hsv_daehne_jaki/**'
+              - 'databases/simplexvirus-db/**'
               - 'databases/stanford-hiv/**'
+              - 'databases/who-influenza/**'
               - 'scripts/respro_build_qc.py'
               - '.github/actions/respro-build-qc/**'
               - '.github/workflows/pr-build-check.yml'
@@ -65,12 +69,15 @@ jobs:
           - name: herpesdrg
             dir: databases/herpesdrg/output
             changed: ${{ needs.detect-changed-databases.outputs.herpesdrg }}
-          - name: hsv_daehne_jaki
-            dir: databases/hsv_daehne_jaki/output
-            changed: ${{ needs.detect-changed-databases.outputs.hsv_daehne_jaki }}
+          - name: simplexvirus-db
+            dir: databases/simplexvirus-db/output
+            changed: ${{ needs.detect-changed-databases.outputs.simplexvirus-db }}
           - name: stanford-hiv
             dir: databases/stanford-hiv/output
             changed: ${{ needs.detect-changed-databases.outputs.stanford-hiv }}
+          - name: who-influenza
+            dir: databases/who-influenza/output
+            changed: ${{ needs.detect-changed-databases.outputs.who-influenza }}
 
     steps:
       - name: Checkout

.github/workflows/hsv-daehne-jaki-autobump.yml → .github/workflows/simplexvirus-db-autobump.yml

@@ -1,4 +1,4 @@
-name: HSV Daehne Jaki Autobump
+name: Simplexvirus DB Autobump
 
 on:
   workflow_dispatch:
@@ -10,7 +10,7 @@ permissions:
   pull-requests: write
 
 jobs:
-  update-hsv-database:
+  update-simplexvirus-db:
     runs-on: ubuntu-latest
 
     steps:
@@ -74,7 +74,7 @@ jobs:
           import sys
 
           latest = "${{ steps.zenodo.outputs.record_id }}"
-          metadata_path = "databases/hsv_daehne_jaki/output/metadata.json"
+          metadata_path = "databases/simplexvirus-db/output/metadata.json"
 
           current = ""
           if os.path.exists(metadata_path):
@@ -103,14 +103,14 @@ jobs:
         if: steps.update_check.outputs.should_update == 'true'
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r databases/hsv_daehne_jaki/scripts/requirements.txt
+          python -m pip install -r databases/simplexvirus-db/scripts/requirements.txt
 
       - name: Run converter
         if: steps.update_check.outputs.should_update == 'true'
         run: |
-          python databases/hsv_daehne_jaki/scripts/convert.py \
+          python databases/simplexvirus-db/scripts/convert.py \
             --source-url "${{ steps.zenodo.outputs.source_url }}" \
-            --output-dir databases/hsv_daehne_jaki/output
+            --output-dir databases/simplexvirus-db/output
 
       - name: Build global metadata manifest
         if: steps.update_check.outputs.should_update == 'true'
@@ -122,8 +122,8 @@ jobs:
         if: steps.update_check.outputs.should_update == 'true'
         uses: ./.github/actions/respro-build-qc
         with:
-          source-name: hsv_daehne_jaki
-          output-dir: databases/hsv_daehne_jaki/output
+          source-name: simplexvirus-db
+          output-dir: databases/simplexvirus-db/output
           work-dir: /tmp/respro_qc
 
       - name: No update detected
@@ -136,10 +136,10 @@ jobs:
         uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          branch: autobump/hsv-daehne-jaki
+          branch: autobump/simplexvirus-db
           delete-branch: true
-          commit-message: "chore(hsv-daehne-jaki): autobump Zenodo outputs"
-          title: "chore: autobump hsv daehne jaki outputs"
+          commit-message: "chore(simplexvirus-db): autobump Zenodo outputs"
+          title: "chore: autobump simplexvirus-db outputs"
           body: |
             Automated monthly update for HSV Daehne/Jaki source data.
 
@@ -153,14 +153,14 @@ jobs:
             This PR was generated by the autobump workflow.
           labels: autobump
           add-paths: |
-            databases/hsv_daehne_jaki/output/rules.tsv
-            databases/hsv_daehne_jaki/output/formula-rules.tsv
-            databases/hsv_daehne_jaki/output/metadata.json
-            databases/hsv_daehne_jaki/output/non-migrated-rules.txt
+            databases/simplexvirus-db/output/rules.tsv
+            databases/simplexvirus-db/output/formula-rules.tsv
+            databases/simplexvirus-db/output/metadata.json
+            databases/simplexvirus-db/output/non-migrated-rules.txt
             databases/manifest.json
 
       - name: Mark workflow failed on respro build error
         if: steps.update_check.outputs.should_update == 'true' && steps.qc.outputs.qc_failed == 'true'
         run: |
-          echo "respro build QC failed for hsv_daehne_jaki; see the PR body and the 'respro build QC' step log."
+          echo "respro build QC failed for simplexvirus-db; see the PR body and the 'respro build QC' step log."
           exit 1

.github/workflows/who-influenza-autobump.yml

@@ -10,9 +10,9 @@ permissions:
   pull-requests: write
 
 env:
-  OUTPUT_DIR: databases/WHO_Influenza/output
+  OUTPUT_DIR: databases/who-influenza/output
   SOURCE_DIR: /tmp/who_source
-  LOOKUP_FILE: databases/WHO_Influenza/scripts/reference-lookup.tsv
+  LOOKUP_FILE: databases/who-influenza/scripts/reference-lookup.tsv
 
 jobs:
   update-who-influenza:
@@ -84,13 +84,13 @@ jobs:
         if: steps.update_check.outputs.should_update == 'true'
         run: |
           set -euo pipefail
-          pip install -r databases/WHO_Influenza/scripts/requirements.txt
+          pip install -r databases/who-influenza/scripts/requirements.txt
 
       - name: Resolve citation DOIs
         if: steps.update_check.outputs.should_update == 'true'
         run: |
           set -euo pipefail
-          python databases/WHO_Influenza/scripts/resolve_references.py \
+          python databases/who-influenza/scripts/resolve_references.py \
             --source-dir "${SOURCE_DIR}" \
             --lookup-file "${LOOKUP_FILE}" \
             --delay 0.5
@@ -99,7 +99,7 @@ jobs:
         if: steps.update_check.outputs.should_update == 'true'
         run: |
           set -euo pipefail
-          python databases/WHO_Influenza/scripts/convert.py \
+          python databases/who-influenza/scripts/convert.py \
             --source-dir "${SOURCE_DIR}" \
             --lookup-file "${LOOKUP_FILE}" \
             --output-dir "${OUTPUT_DIR}"
@@ -114,8 +114,8 @@ jobs:
         if: steps.update_check.outputs.should_update == 'true'
         uses: ./.github/actions/respro-build-qc
         with:
-          source-name: WHO_Influenza
-          output-dir: databases/WHO_Influenza/output
+          source-name: who-influenza
+          output-dir: databases/who-influenza/output
           work-dir: /tmp/respro_qc
 
       - name: No update detected
@@ -130,7 +130,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
           branch: autobump/who-influenza
           delete-branch: true
-          commit-message: "chore(WHO_Influenza): autobump source outputs"
+          commit-message: "chore(who-influenza): autobump source outputs"
           title: "chore: autobump WHO Influenza outputs"
           body: |
             Automated monthly update for the WHO influenza marker tables.
@@ -144,16 +144,16 @@ jobs:
             This PR was generated by the autobump workflow.
           labels: autobump
           add-paths: |
-            databases/WHO_Influenza/output/rules.tsv
-            databases/WHO_Influenza/output/formula-rules.tsv
-            databases/WHO_Influenza/output/metadata.json
-            databases/WHO_Influenza/output/non-migrated-rules.txt
-            databases/WHO_Influenza/output/source-state.json
-            databases/WHO_Influenza/scripts/reference-lookup.tsv
+            databases/who-influenza/output/rules.tsv
+            databases/who-influenza/output/formula-rules.tsv
+            databases/who-influenza/output/metadata.json
+            databases/who-influenza/output/non-migrated-rules.txt
+            databases/who-influenza/output/source-state.json
+            databases/who-influenza/scripts/reference-lookup.tsv
             databases/manifest.json
 
       - name: Mark workflow failed on respro build error
         if: steps.update_check.outputs.should_update == 'true' && steps.qc.outputs.qc_failed == 'true'
         run: |
-          echo "respro build QC failed for WHO_Influenza; see the PR body and the 'respro build QC' step log."
+          echo "respro build QC failed for who-influenza; see the PR body and the 'respro build QC' step log."
           exit 1

databases/manifest.json

@@ -1,25 +1,6 @@
 {
   "respro_version": ">=0.2.0",
   "databases": [
-    {
-      "source_name": "WHO_Influenza",
-      "metadata_path": "databases/WHO_Influenza/output/metadata.json",
-      "rules_path": "databases/WHO_Influenza/output/rules.tsv",
-      "formula_rules_path": "databases/WHO_Influenza/output/formula-rules.tsv",
-      "example_fasta_path": "databases/WHO_Influenza/example/example.fasta",
-      "metadata": {
-        "maintainers": [
-          "Expert Working Group on Antiviral Susceptibility"
-        ],
-        "contact": "gisrs-whohq@who.int",
-        "publication_pmid": "",
-        "website": "https://www.who.int/teams/global-influenza-programme/laboratory-network/quality-assurance/antiviral-susceptibility-influenza",
-        "description": "WHO influenza antiviral susceptibility marker tables: neuraminidase inhibitor resistance markers for human and avian influenza viruses and polymerase acidic (PA) baloxavir markers, curated from the WHO marker tables.",
-        "maintainer_update": "2026-07-17",
-        "license": "CC-BY-NC-SA-3.0-IGO",
-        "tsv_checksum": "sha256:19f0a6149ed1bfb13c130eb381747bf0f03694b3f7e19a38f164d3cfe60b01f5"
-      }
-    },
     {
       "source_name": "charmd",
       "metadata_path": "databases/charmd/output/metadata.json",
@@ -60,11 +41,11 @@
       }
     },
     {
-      "source_name": "hsv_daehne_jaki",
-      "metadata_path": "databases/hsv_daehne_jaki/output/metadata.json",
-      "rules_path": "databases/hsv_daehne_jaki/output/rules.tsv",
-      "formula_rules_path": "databases/hsv_daehne_jaki/output/formula-rules.tsv",
-      "example_fasta_path": "databases/hsv_daehne_jaki/example/example.fasta",
+      "source_name": "simplexvirus-db",
+      "metadata_path": "databases/simplexvirus-db/output/metadata.json",
+      "rules_path": "databases/simplexvirus-db/output/rules.tsv",
+      "formula_rules_path": "databases/simplexvirus-db/output/formula-rules.tsv",
+      "example_fasta_path": "databases/simplexvirus-db/example/example.fasta",
       "metadata": {
         "maintainers": [
           "Daehne, Theo",
@@ -98,6 +79,25 @@
         "license": "GNU General Public License v3.0",
         "tsv_checksum": "sha256:6b893a9939c0c82cf8fb2c77f2cccb6cac12fe89ee960397c6798c3b078d0256"
       }
+    },
+    {
+      "source_name": "who-influenza",
+      "metadata_path": "databases/who-influenza/output/metadata.json",
+      "rules_path": "databases/who-influenza/output/rules.tsv",
+      "formula_rules_path": "databases/who-influenza/output/formula-rules.tsv",
+      "example_fasta_path": "databases/who-influenza/example/example.fasta",
+      "metadata": {
+        "maintainers": [
+          "Expert Working Group on Antiviral Susceptibility"
+        ],
+        "contact": "gisrs-whohq@who.int",
+        "publication_pmid": "",
+        "website": "https://www.who.int/teams/global-influenza-programme/laboratory-network/quality-assurance/antiviral-susceptibility-influenza",
+        "description": "WHO influenza antiviral susceptibility marker tables: neuraminidase inhibitor resistance markers for human and avian influenza viruses and polymerase acidic (PA) baloxavir markers, curated from the WHO marker tables.",
+        "maintainer_update": "2026-07-17",
+        "license": "CC-BY-NC-SA-3.0-IGO",
+        "tsv_checksum": "sha256:19f0a6149ed1bfb13c130eb381747bf0f03694b3f7e19a38f164d3cfe60b01f5"
+      }
     }
   ]
 }

databases/who-influenza/example/example.fasta

@@ -0,0 +1,22 @@
+>OP010240.1 Influenza A virus (A/West Virginia/20/2022(H1N1)) segment 6 neuraminidase (NA) gene, complete cds
+AGTTTAAAATGAATCCAAACCAAAAGATAATAACCATTGGTTCTATCTGTATGGCAATTGGAACGGCTAA
+CTTAATATTGCAAATTGGAAACATAATCTCAATATGGGTTAGCCACTCAATTCAAATTGGAAATCAAAGC
+CAGATTGAAACATGCAATAAAAGCGTCATTACTTATGAAAACAACACTTGGGTAAATCAGACATTTGTTA
+ACATCAGCAACACTAACTCTGCTGCTAGACATTCAGTGGCTTCCGTGAAATTAGCGGGCAATTCCTCTCT
+CTGCCCTGTTAGTGGATGGGCTATATATAGTAAAGACAACAGTGTAAGAATCGGTTCCAAGGGGGATGTG
+TTTGTCATAAGGGAACCATTCATATCATGCTCTCCCTTGGAATGCAGAACCTTCTTCTTGACTCAAGGGG
+CTTTGCTAAATGACAAACATTCCAATGGAACCATTAAAGACAGAAGCCCATACCGAACCCTAATGAGCTG
+TCCTATTGGTGAAGTTCCCTCTCCATACAACTCAAGATTTGAGTCAGTTGCTTGGTCAGCAAGTGCTTGT
+CATGATGGCACCAATTGGCTAACAATTGGAATTTCTGGCCCAGACAATGGGGCAGTGGCTGTGTTGAAAT
+ACAATGGCATAATAACAGACACTATCAAGAGTTGGAGGAACAAGATATTGAGAACACAAGAGTCTGAATG
+TGCATGTGTAAATGGTTCTTGCTTTACCATAATGACCGATGGACCAAGTGATGGACAGGCCTCATACAAA
+ATCTTCAGAATAGAAAAGGGAAAGATAATCAAATCAGTCGAAATGAAAGCCCCTAATTACTACTATGAAG
+AATGCTCCTGTTACCCTGATTCTAGTGAAATCACATGTGTGTGCAGGGATAACTGGCATGGCTCGAATCG
+ACCGTGGGTGTCTTTCAACCAGAATCTGGAATATCAGATGGGATACATATGCAGTGGGGTTTTCGGAGAC
+AATCCACGCCCTAATGATAAGACAGGCAGTTGTGGTCCAGTATCGTCTAATGGAGCAAATGGGGTAAAAG
+GATTTTCATTCAAATACGGCAATGGTGTTTGGATAGGGAGAACTAAGAGCATTAATTCAAGAAAAGGTTT
+TGAGATGATTTGGGATCCGAATGGATGGACTGGGACTGACAATAAATTCTCAAAAAAGCAAGATATCGTA
+GGAATAAATGAGTGGTCAGGGTATAGCGGGAGTTTTGTTCAGCATCCAGAACTAACAGGGCTGAATTGTA
+TAAGACCTTGCTTCTGGGTTGAACTAATAAGAGGACGACCCGAAGAGAACACAATCTGGACTAGCGGGAG
+CAGCATATCCTTTTGTGGTGTAGACAGTGACATTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCA
+TTTACCATTGACAAGTAATTTGTTCAAAAAACT

databases/WHO_Influenza/output/metadata.json → databases/who-influenza/output/metadata.json

@@ -8,5 +8,11 @@
   "description": "WHO influenza antiviral susceptibility marker tables: neuraminidase inhibitor resistance markers for human and avian influenza viruses and polymerase acidic (PA) baloxavir markers, curated from the WHO marker tables.",
   "maintainer_update": "2026-07-17",
   "license": "CC-BY-NC-SA-3.0-IGO",
-  "tsv_checksum": "sha256:19f0a6149ed1bfb13c130eb381747bf0f03694b3f7e19a38f164d3cfe60b01f5"
+  "tsv_checksum": "sha256:19f0a6149ed1bfb13c130eb381747bf0f03694b3f7e19a38f164d3cfe60b01f5",
+  "interpretation_algorithms": [
+    {
+      "name": "drug_interpretation",
+      "method": "by_phenotype"
+    }
+  ]
 }

databases/WHO_Influenza/scripts/convert.py → databases/who-influenza/scripts/convert.py

@@ -1169,6 +1169,12 @@ def tsv_from_rows(rows: list[dict], columns: list[str]) -> str:
         "tsv_checksum": "sha256:" + hashlib.sha256(
             rules_content.encode("utf-8")
         ).hexdigest(),
+        "interpretation_algorithms": [
+            {
+                "name": "drug_interpretation",
+                "method": "by_phenotype",
+            },
+        ],
     }
     metadata_path = out_dir / "metadata.json"
     metadata_path.write_text(

databases/WHO_Influenza/tests/test_convert.py → databases/who-influenza/tests/test_convert.py

@@ -1,4 +1,4 @@
-"""Tests for WHO Influenza conversion logic (databases/WHO_Influenza)."""
+"""Tests for WHO Influenza conversion logic (databases/who-influenza)."""
 
 import sys
 from pathlib import Path