From 97245e65ba7e74cc6c1772afb185301e355f1ee7 Mon Sep 17 00:00:00 2001 From: jonas Date: Fri, 9 Oct 2026 13:13:54 +0200 Subject: [PATCH] renamed and added algorithm to who --- .github/workflows/pr-build-check.yml | 21 +++++--- ...obump.yml => simplexvirus-db-autobump.yml} | 32 ++++++------- .github/workflows/who-influenza-autobump.yml | 30 ++++++------ databases/WHO_Influenza/example/example.fasta | 22 --------- databases/manifest.json | 48 +++++++++---------- .../example/example.fasta | 0 .../output/formula-rules.tsv | 0 .../output/metadata.json | 0 .../output/non-migrated-rules.txt | 0 .../output/rules.tsv | 0 .../scripts/convert.py | 0 .../scripts/requirements.txt | 0 databases/who-influenza/example/example.fasta | 22 +++++++++ .../output/formula-rules.tsv | 0 .../output/metadata.json | 8 +++- .../output/non-migrated-rules.txt | 0 .../output/rules.tsv | 0 .../output/source-state.json | 0 .../scripts/convert.py | 6 +++ .../scripts/reference-lookup.tsv | 0 .../scripts/references/AB292780.fasta | 0 .../scripts/references/AY207514.fasta | 0 .../scripts/references/CY098534.1.fasta | 0 .../scripts/references/CY115257.fasta | 0 .../scripts/references/CY115260.fasta | 0 .../scripts/references/EF619973.fasta | 0 .../scripts/references/KX297920.1.fasta | 0 .../scripts/references/MW287218.1.fasta | 0 .../scripts/references/MW287220.1.fasta | 0 .../scripts/references/MW325955.1.fasta | 0 .../scripts/references/NC_007368.fasta | 0 .../scripts/references/NC_026429.fasta | 0 .../scripts/references/NC_026434.fasta | 0 .../scripts/references/NC_026437.fasta | 0 .../scripts/requirements.txt | 0 .../scripts/resolve_references.py | 0 .../scripts/who_parsers.py | 0 .../tests/test_convert.py | 2 +- 38 files changed, 105 insertions(+), 86 deletions(-) rename .github/workflows/{hsv-daehne-jaki-autobump.yml => simplexvirus-db-autobump.yml} (85%) delete mode 100644 databases/WHO_Influenza/example/example.fasta rename databases/{hsv_daehne_jaki => simplexvirus-db}/example/example.fasta (100%) rename databases/{hsv_daehne_jaki => simplexvirus-db}/output/formula-rules.tsv (100%) rename databases/{hsv_daehne_jaki => simplexvirus-db}/output/metadata.json (100%) rename databases/{hsv_daehne_jaki => simplexvirus-db}/output/non-migrated-rules.txt (100%) rename databases/{hsv_daehne_jaki => simplexvirus-db}/output/rules.tsv (100%) rename databases/{hsv_daehne_jaki => simplexvirus-db}/scripts/convert.py (100%) rename databases/{hsv_daehne_jaki => simplexvirus-db}/scripts/requirements.txt (100%) create mode 100644 databases/who-influenza/example/example.fasta rename databases/{WHO_Influenza => who-influenza}/output/formula-rules.tsv (100%) rename databases/{WHO_Influenza => who-influenza}/output/metadata.json (81%) rename databases/{WHO_Influenza => who-influenza}/output/non-migrated-rules.txt (100%) rename databases/{WHO_Influenza => who-influenza}/output/rules.tsv (100%) rename databases/{WHO_Influenza => who-influenza}/output/source-state.json (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/convert.py (99%) rename databases/{WHO_Influenza => who-influenza}/scripts/reference-lookup.tsv (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/AB292780.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/AY207514.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/CY098534.1.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/CY115257.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/CY115260.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/EF619973.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/KX297920.1.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/MW287218.1.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/MW287220.1.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/MW325955.1.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/NC_007368.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/NC_026429.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/NC_026434.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/references/NC_026437.fasta (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/requirements.txt (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/resolve_references.py (100%) rename databases/{WHO_Influenza => who-influenza}/scripts/who_parsers.py (100%) rename databases/{WHO_Influenza => who-influenza}/tests/test_convert.py (99%) diff --git a/.github/workflows/pr-build-check.yml b/.github/workflows/pr-build-check.yml index 349f7b5..52fd607 100644 --- a/.github/workflows/pr-build-check.yml +++ b/.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: ${{ needs.detect-changed-databases.outputs.who-influenza }} steps: - name: Checkout diff --git a/.github/workflows/hsv-daehne-jaki-autobump.yml b/.github/workflows/simplexvirus-db-autobump.yml similarity index 85% rename from .github/workflows/hsv-daehne-jaki-autobump.yml rename to .github/workflows/simplexvirus-db-autobump.yml index f2b7444..ce233ab 100644 --- a/.github/workflows/hsv-daehne-jaki-autobump.yml +++ b/.github/workflows/simplexvirus-db-autobump.yml @@ -1,4 +1,4 @@ -name: HSV Daehne Jaki Autobump +name: Simplexvirus DB Autobump on: workflow_dispatch: @@ -10,7 +10,7 @@ permissions: pull-requests: write jobs: - update-hsv-database: + update-simplexvirus-db: runs-on: ubuntu-latest steps: @@ -74,7 +74,7 @@ jobs: import sys latest = "${{ 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 diff --git a/.github/workflows/who-influenza-autobump.yml b/.github/workflows/who-influenza-autobump.yml index 2391004..68a2b38 100644 --- a/.github/workflows/who-influenza-autobump.yml +++ b/.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 diff --git a/databases/WHO_Influenza/example/example.fasta b/databases/WHO_Influenza/example/example.fasta deleted file mode 100644 index 609f51d..0000000 --- a/databases/WHO_Influenza/example/example.fasta +++ /dev/null @@ -1,22 +0,0 @@ ->KJ439218.1 Influenza A virus (A/Gainesville/01/2014(H3N2)) segment 6 neuraminidase (NA) gene, complete cds -ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCTTCA -TGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTTAAGCAATATGAATTCAACTCCCCCCCAAA -CAACCAAGTGATGCTGTGTGAACCAACAATAATGGAAAGAAACATAACAGAGATAGTGTATCTAACCAAC -ACCACCATAGAGAAGGAAATATGCCCCAAACCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGGCA -TTACAGGATTTGCACCTTTCTCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGAC -AAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA -AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACTCTATTGATGAATGAGTTGG -GTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAA -AGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAATGCAACTGCTAGCTTCATTTACAATGGGAGG -CTTGTAGATAGTGTTGTTTCATGGTCCAAAGAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCA -ATGGAACTTGTACAGTAGTAATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCAT -TGAGGAGGGGAAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAAGAGTGCTCTTGC -TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATCGGCCCATCGTAG -ATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGACTTGTTGGAGACACACCCAG -AAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGGTCCTAACAATGAAGAAGGTGGTCATGGAGTGAAA -GGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGAAGAACAATCAACGAGACGTCACGCTTAGGGT -ATGAAACCTTCAAAGTCATTGAAGGCTGGTCCAATCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCAT -AGTTGACAGAGGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG -TGCTTTTATGTAGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCAAACAGTATTG -TTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACCTCAATCTCAT -GCCTATATAA \ No newline at end of file diff --git a/databases/manifest.json b/databases/manifest.json index 038e97c..8aaf173 100644 --- a/databases/manifest.json +++ b/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" + } } ] } diff --git a/databases/hsv_daehne_jaki/example/example.fasta b/databases/simplexvirus-db/example/example.fasta similarity index 100% rename from databases/hsv_daehne_jaki/example/example.fasta rename to databases/simplexvirus-db/example/example.fasta diff --git a/databases/hsv_daehne_jaki/output/formula-rules.tsv b/databases/simplexvirus-db/output/formula-rules.tsv similarity index 100% rename from databases/hsv_daehne_jaki/output/formula-rules.tsv rename to databases/simplexvirus-db/output/formula-rules.tsv diff --git a/databases/hsv_daehne_jaki/output/metadata.json b/databases/simplexvirus-db/output/metadata.json similarity index 100% rename from databases/hsv_daehne_jaki/output/metadata.json rename to databases/simplexvirus-db/output/metadata.json diff --git a/databases/hsv_daehne_jaki/output/non-migrated-rules.txt b/databases/simplexvirus-db/output/non-migrated-rules.txt similarity index 100% rename from databases/hsv_daehne_jaki/output/non-migrated-rules.txt rename to databases/simplexvirus-db/output/non-migrated-rules.txt diff --git a/databases/hsv_daehne_jaki/output/rules.tsv b/databases/simplexvirus-db/output/rules.tsv similarity index 100% rename from databases/hsv_daehne_jaki/output/rules.tsv rename to databases/simplexvirus-db/output/rules.tsv diff --git a/databases/hsv_daehne_jaki/scripts/convert.py b/databases/simplexvirus-db/scripts/convert.py similarity index 100% rename from databases/hsv_daehne_jaki/scripts/convert.py rename to databases/simplexvirus-db/scripts/convert.py diff --git a/databases/hsv_daehne_jaki/scripts/requirements.txt b/databases/simplexvirus-db/scripts/requirements.txt similarity index 100% rename from databases/hsv_daehne_jaki/scripts/requirements.txt rename to databases/simplexvirus-db/scripts/requirements.txt diff --git a/databases/who-influenza/example/example.fasta b/databases/who-influenza/example/example.fasta new file mode 100644 index 0000000..5b8b2fe --- /dev/null +++ b/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 \ No newline at end of file diff --git a/databases/WHO_Influenza/output/formula-rules.tsv b/databases/who-influenza/output/formula-rules.tsv similarity index 100% rename from databases/WHO_Influenza/output/formula-rules.tsv rename to databases/who-influenza/output/formula-rules.tsv diff --git a/databases/WHO_Influenza/output/metadata.json b/databases/who-influenza/output/metadata.json similarity index 81% rename from databases/WHO_Influenza/output/metadata.json rename to databases/who-influenza/output/metadata.json index 266a0d6..211544e 100644 --- a/databases/WHO_Influenza/output/metadata.json +++ b/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" + } + ] } diff --git a/databases/WHO_Influenza/output/non-migrated-rules.txt b/databases/who-influenza/output/non-migrated-rules.txt similarity index 100% rename from databases/WHO_Influenza/output/non-migrated-rules.txt rename to databases/who-influenza/output/non-migrated-rules.txt diff --git a/databases/WHO_Influenza/output/rules.tsv b/databases/who-influenza/output/rules.tsv similarity index 100% rename from databases/WHO_Influenza/output/rules.tsv rename to databases/who-influenza/output/rules.tsv diff --git a/databases/WHO_Influenza/output/source-state.json b/databases/who-influenza/output/source-state.json similarity index 100% rename from databases/WHO_Influenza/output/source-state.json rename to databases/who-influenza/output/source-state.json diff --git a/databases/WHO_Influenza/scripts/convert.py b/databases/who-influenza/scripts/convert.py similarity index 99% rename from databases/WHO_Influenza/scripts/convert.py rename to databases/who-influenza/scripts/convert.py index 0d745fb..7db651f 100644 --- a/databases/WHO_Influenza/scripts/convert.py +++ b/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( diff --git a/databases/WHO_Influenza/scripts/reference-lookup.tsv b/databases/who-influenza/scripts/reference-lookup.tsv similarity index 100% rename from databases/WHO_Influenza/scripts/reference-lookup.tsv rename to databases/who-influenza/scripts/reference-lookup.tsv diff --git a/databases/WHO_Influenza/scripts/references/AB292780.fasta b/databases/who-influenza/scripts/references/AB292780.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/AB292780.fasta rename to databases/who-influenza/scripts/references/AB292780.fasta diff --git a/databases/WHO_Influenza/scripts/references/AY207514.fasta b/databases/who-influenza/scripts/references/AY207514.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/AY207514.fasta rename to databases/who-influenza/scripts/references/AY207514.fasta diff --git a/databases/WHO_Influenza/scripts/references/CY098534.1.fasta b/databases/who-influenza/scripts/references/CY098534.1.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/CY098534.1.fasta rename to databases/who-influenza/scripts/references/CY098534.1.fasta diff --git a/databases/WHO_Influenza/scripts/references/CY115257.fasta b/databases/who-influenza/scripts/references/CY115257.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/CY115257.fasta rename to databases/who-influenza/scripts/references/CY115257.fasta diff --git a/databases/WHO_Influenza/scripts/references/CY115260.fasta b/databases/who-influenza/scripts/references/CY115260.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/CY115260.fasta rename to databases/who-influenza/scripts/references/CY115260.fasta diff --git a/databases/WHO_Influenza/scripts/references/EF619973.fasta b/databases/who-influenza/scripts/references/EF619973.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/EF619973.fasta rename to databases/who-influenza/scripts/references/EF619973.fasta diff --git a/databases/WHO_Influenza/scripts/references/KX297920.1.fasta b/databases/who-influenza/scripts/references/KX297920.1.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/KX297920.1.fasta rename to databases/who-influenza/scripts/references/KX297920.1.fasta diff --git a/databases/WHO_Influenza/scripts/references/MW287218.1.fasta b/databases/who-influenza/scripts/references/MW287218.1.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/MW287218.1.fasta rename to databases/who-influenza/scripts/references/MW287218.1.fasta diff --git a/databases/WHO_Influenza/scripts/references/MW287220.1.fasta b/databases/who-influenza/scripts/references/MW287220.1.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/MW287220.1.fasta rename to databases/who-influenza/scripts/references/MW287220.1.fasta diff --git a/databases/WHO_Influenza/scripts/references/MW325955.1.fasta b/databases/who-influenza/scripts/references/MW325955.1.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/MW325955.1.fasta rename to databases/who-influenza/scripts/references/MW325955.1.fasta diff --git a/databases/WHO_Influenza/scripts/references/NC_007368.fasta b/databases/who-influenza/scripts/references/NC_007368.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/NC_007368.fasta rename to databases/who-influenza/scripts/references/NC_007368.fasta diff --git a/databases/WHO_Influenza/scripts/references/NC_026429.fasta b/databases/who-influenza/scripts/references/NC_026429.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/NC_026429.fasta rename to databases/who-influenza/scripts/references/NC_026429.fasta diff --git a/databases/WHO_Influenza/scripts/references/NC_026434.fasta b/databases/who-influenza/scripts/references/NC_026434.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/NC_026434.fasta rename to databases/who-influenza/scripts/references/NC_026434.fasta diff --git a/databases/WHO_Influenza/scripts/references/NC_026437.fasta b/databases/who-influenza/scripts/references/NC_026437.fasta similarity index 100% rename from databases/WHO_Influenza/scripts/references/NC_026437.fasta rename to databases/who-influenza/scripts/references/NC_026437.fasta diff --git a/databases/WHO_Influenza/scripts/requirements.txt b/databases/who-influenza/scripts/requirements.txt similarity index 100% rename from databases/WHO_Influenza/scripts/requirements.txt rename to databases/who-influenza/scripts/requirements.txt diff --git a/databases/WHO_Influenza/scripts/resolve_references.py b/databases/who-influenza/scripts/resolve_references.py similarity index 100% rename from databases/WHO_Influenza/scripts/resolve_references.py rename to databases/who-influenza/scripts/resolve_references.py diff --git a/databases/WHO_Influenza/scripts/who_parsers.py b/databases/who-influenza/scripts/who_parsers.py similarity index 100% rename from databases/WHO_Influenza/scripts/who_parsers.py rename to databases/who-influenza/scripts/who_parsers.py diff --git a/databases/WHO_Influenza/tests/test_convert.py b/databases/who-influenza/tests/test_convert.py similarity index 99% rename from databases/WHO_Influenza/tests/test_convert.py rename to databases/who-influenza/tests/test_convert.py index 67908be..6ee0810 100644 --- a/databases/WHO_Influenza/tests/test_convert.py +++ b/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