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sha256:1265fb8410cff3cc2a86b05cd83b76fb72bb4993bc757491be3dca123da02f62 +size 18134169291 diff --git a/manifest.yaml b/manifest.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d5ce068302e569f2fae9644ec5128a2ba0b3c75d --- /dev/null +++ b/manifest.yaml @@ -0,0 +1,290 @@ +onescience_manifest_version: "0.1" +resource_type: dataset +resource: + id: OneScience/AlphaFold3_dataset + name: AlphaFold3_dataset + domain: bio + domain_tags: [bio, biosciences, protein_structure, msa_database] + task: alphafold3_inference_database + task_tags: [inference_input, msa_search, template_search, data_pipeline] + modalities: [protein_sequence, msa, template_database, alphafold3_json] + input_formats: [alphafold3_json, fasta, mmcif, mmseqs_db] + output_formats: [alphafold3_json] + summary: AlphaFold3 运行所需的数据集资源，包含推理输入样例、公共数据库、MMseqs 数据库、Jackhmmer 分片数据库和对齐相关目录。 + +platform_resource: + primary: + platform: modelscope + repo_id: OneScience/AlphaFold3_dataset + repo_type: dataset + url: https://modelscope.cn/datasets/OneScience/AlphaFold3_dataset + revision: main + readme_path: README.md + manifest_path: manifest.yaml + mirrors: [] + access: + visibility: public + license: follows upstream database and AlphaFold3 data licenses + +website_integration: + enabled: true + click_target: + platform: modelscope + resource_url: https://modelscope.cn/datasets/OneScience/AlphaFold3_dataset + llm_handoff: + readme_required: true + manifest_required: true + download_readme_first: true + resolve_related_models: true + default_run_goal: dataset_validation + cwd_after_download: 下载后切换到数据集包根目录再运行验证命令；如果使用 --cache_dir，cwd 应为实际下载出的 OneScience/AlphaFold3_dataset 包根目录。 + +runtime: + enabled: true + onescience_domain: bio + min_onescience_version: null + supported_execution: [local, local_slurm, remote_slurm, scnet_mcp] + +onescience: + repo: https://gitee.com/onescience-ai/onescience + official_links: + gitee: + doc: https://gitee.com/onescience-ai/onescience-doc + onescience: https://gitee.com/onescience-ai/onescience + skills: https://gitee.com/onescience-ai/oneskills + github: + doc: https://github.com/onescience-ai/OneScience-doc + onescience: https://github.com/onescience-ai/OneScience + skills: https://github.com/onescience-ai/oneskills + install: + required_by_default: false + command: bash install.sh bio + source_paths: [] + compatibility: + examples_path: examples/biosciences/alphafold3 + status: examples_compatible + +runtime_package: + kind: standard_runtime_package + package_root: . + standard_layout: + workdir: . + config_dir: metadata + checkpoint_dir: null + data_dir: data + output_dir: outputs + apply_policy: + mode: direct_use + target: session_workdir + overwrite: true + protect_installed_onescience: true + entry_files: + - metadata/file_manifest.yaml + - scripts/validate_dataset.py + entrypoints: + preflight: scripts/validate_dataset.py + inference: null + train: null + finetune: null + evaluate: null + visualize: null + deploy: null + +files: + model_files: [] + dataset_files: + - id: infer_input_data + path: data/infer_input_data/ + role: inference_input + format: alphafold3_json + description_zh: AlphaFold3 JSON 推理输入样例，包含 all_data 和 pressure_data 子目录。 + required: true + required_for: [preflight, minimal_inference] + source: + platform: modelscope + repo_id: OneScience/AlphaFold3_dataset + repo_type: dataset + path: data/infer_input_data/ + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: data/infer_input_data/ + integrity_manifest: metadata/file_manifest.yaml + - id: public_databases + path: data/public_databases/ + role: database + format: fasta_mmcif + description_zh: Jackhmmer 和模板搜索所需公共数据库，包括 BFD、MGnify、UniRef90、UniProt、RNA、PDB seqres；上传视图用 pdb_2022_09_28_mmcif_files.tar 提供 mmCIF 文件，运行模板搜索前需解包为 mmcif_files 目录。 + required: true + required_for: [data_pipeline, jackhmmer_search] + local_path: data/public_databases/ + integrity_manifest: metadata/file_manifest.yaml + - id: mmseqs_db + path: data/mmseqsDB/ + role: database + format: mmseqs_db + description_zh: MMseqs 搜索所需数据库，包含 small_bfd、mgnify、uniprot_cluster_annot 和 uniref90 数据库。 + required: true + required_for: [mmseqs_search] + local_path: data/mmseqsDB/ + integrity_manifest: metadata/file_manifest.yaml + - id: jackhmmer_split + path: data/jackhmmer_split/ + role: database + format: sharded_fasta + description_zh: Jackhmmer 搜索用分片 FASTA 数据库。 + required: true + required_for: [jackhmmer_search] + local_path: data/jackhmmer_split/ + integrity_manifest: metadata/file_manifest.yaml + - id: align_db + path: data/alignDB/ + role: database + format: fasta + description_zh: 对齐相关数据库目录。 + required: false + required_for: [advanced_pipeline] + local_path: data/alignDB/ + config_files: + - id: file_manifest + path: metadata/file_manifest.yaml + role: integrity_manifest + description_zh: 记录整理后链接数据与原始数据之间的文件名、大小和 SHA256 校验信息。 + required: true + required_for: [preflight] + sample_files: + - id: sample_7r6r + path: data/infer_input_data/all_data/7r6r_data.json + role: inference_input + description_zh: 带 MSA 的最小推理样例。 + required: true + required_for: [dataset_validation, minimal_inference] + script_files: + - id: validate_dataset + path: scripts/validate_dataset.py + role: preflight + description_zh: 检查数据目录、样例 JSON 可读性、关键文件名、大小和 SHA256。 + required: true + required_for: [preflight] + +dataset: + format: [alphafold3_json, fasta, mmcif, mmseqs_db, sharded_fasta] + sample_unit: 一个 AlphaFold3 JSON fold input 或一个搜索数据库分片。 + schema: + path: metadata/file_manifest.yaml + json_required_fields: [dialect, version, name, sequences] + splits: + inference_all_data: data/infer_input_data/all_data/ + inference_pressure_data: data/infer_input_data/pressure_data/ + public_databases: data/public_databases/ + mmseqs: data/mmseqsDB/ + jackhmmer_split: data/jackhmmer_split/ + +relations: + required_datasets: [] + optional_datasets: [] + compatible_models: + - id: OneScience/AlphaFold3/ + role: inference_input_and_database + required_for: [preflight, inference, data_pipeline, msa_search] + resource_ref: + platform: modelscope + repo_id: OneScience/AlphaFold3/ + repo_type: model + url: https://modelscope.cn/models/OneScience/AlphaFold3/ + revision: main + readme_path: README.md + manifest_path: manifest.yaml + expected_local_path: data/alphafold3_dataset + adapter: null + +run_matrix: + scenarios: + - name: dataset_validation + default: true + goal: minimal_validation + capability: preflight + required_model_files: [] + required_dataset_files: [infer_input_data, public_databases, mmseqs_db, jackhmmer_split] + required_config_files: [file_manifest] + required_datasets: [] + command_refs: [commands.preflight.validate_dataset] + outputs: [dataset_validation_stdout] + prerequisites: + - cwd 为数据集包根目录。 + - name: provide_data_to_alphafold3_model + capability: data_pipeline + required_model_files: [] + required_dataset_files: [infer_input_data, public_databases, mmseqs_db, jackhmmer_split] + required_config_files: [file_manifest] + required_datasets: [] + command_refs: [commands.prepare.link_into_model_package] + outputs: [model_expected_dataset_path] + prerequisites: + - 已下载 OneScience/AlphaFold3/ 模型包。 + +capabilities: + inference: false + train: false + finetune: false + evaluate: false + visualize: false + deploy: false + preflight: true + data_pipeline: true + +commands: + download: + - name: download_dataset + cwd: . + command: "modelscope download --dataset OneScience/AlphaFold3_dataset" + description_zh: 下载 AlphaFold3 数据集标准仓库。 + - name: download_model + cwd: . + command: "modelscope download --model OneScience/AlphaFold3/" + description_zh: 下载适配模型仓库。 + prepare: + - name: link_into_model_package + cwd: . + command: "mkdir -p /path/to/model_package/data && ln -s $(pwd)/data /path/to/model_package/data/alphafold3_dataset" + description_zh: 将数据集包的 data 子目录链接到模型包期望的数据路径。 + preflight: + - name: validate_dataset + cwd: . + command: "python scripts/validate_dataset.py --root ." + description_zh: 验证数据目录、JSON 样例和关键文件完整性。 + inference: [] + train: [] + finetune: [] + evaluate: [] + visualize: [] + deploy: [] + +expected_outputs: + - id: dataset_validation_stdout + path: stdout + description_zh: "输出 dataset_validation_ok: true。" + - id: model_expected_dataset_path + path: /path/to/model_package/data/alphafold3_dataset + description_zh: 模型包可通过该路径访问数据集。 + +diagnostics: + - symptom: dataset_id_mismatch + cause_zh: README、manifest 或下载命令中的数据集 ID 与 OneScience/AlphaFold3_dataset 不一致。 + action_zh: 统一改为 OneScience/AlphaFold3_dataset。 + - symptom: missing_infer_input_data + cause_zh: 数据集目录未完整下载或 cwd 不在数据集包根目录。 + action_zh: 重新执行 modelscope download --dataset OneScience/AlphaFold3_dataset 并切换到下载后的数据集包根目录。 + - symptom: sha256_mismatch + cause_zh: 整理后的链接或复制文件与原始数据不一致。 + action_zh: 对照 metadata/file_manifest.yaml 的 source_path 重新整理对应文件。 + - symptom: mmseqs_database_missing + cause_zh: data/mmseqsDB 下缺少 small_bfd_db、mgnify_db、uniprot_cluster_annot_db 或 uniref90_db。 + action_zh: 检查数据集下载是否完整，或重新建立指向原始 mmseqsDB 的链接。 + +domain_extension: + bio: + molecule_types: [protein, rna, dna, ligand] + database_roles: [msa_search, template_search] + supported_search_backends: [mmseqs, jackhmmer] + json_schema_required_fields: [dialect, version, name, sequences] diff --git a/metadata/file_manifest.yaml b/metadata/file_manifest.yaml new file mode 100644 index 0000000000000000000000000000000000000000..804f1fff7618ed0c1dbb51c4037994e5da80fb2f --- /dev/null +++ b/metadata/file_manifest.yaml @@ -0,0 +1,49 @@ +source_root: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3 +linked_root: data +link_policy: absolute_symlink_to_original_readonly_source +dataset_directories: + - path: data/infer_input_data + role: inference_inputs + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/infer_input_data + - path: data/public_databases + role: jackhmmer_public_databases + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/public_databases + - path: data/mmseqsDB + role: mmseqs_databases + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/mmseqsDB + - path: data/jackhmmer_split + role: sharded_jackhmmer_databases + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/jackhmmer_split + - path: data/alignDB + role: alignment_database + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/alignDB +verified_file_count: 7 +files: + - path: data/infer_input_data/readme.md + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/infer_input_data/readme.md + size_bytes: 3331 + sha256: 41e8f236db5423c78c6b9c16709bec1eb408a06124840232e7537c14ff220fe7 + - path: data/infer_input_data/all_data/7r6r_data.json + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/infer_input_data/all_data/7r6r_data.json + size_bytes: 1216061 + sha256: 04a178d3977b9b150c10f9d284ca6b3179924aecbd7659906071e79a3dec0632 + - path: data/infer_input_data/all_data/t1119_data.json + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/infer_input_data/all_data/t1119_data.json + size_bytes: 613027 + sha256: 5176bd907cf73e09a764a646cb6dd8afb24fc0b43285b863a075814b067c3d60 + - path: data/mmseqsDB/small_bfd_db.dbtype + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/mmseqsDB/small_bfd_db.dbtype + size_bytes: 4 + sha256: c9c7e8c63836a93f6d8c04598b6503d2863a2df7b86366157178234175704dcc + - path: data/mmseqsDB/small_bfd_db.source + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/mmseqsDB/small_bfd_db.source + size_bytes: 42 + sha256: f428f2ebedffed4eeb10c8bf95fc814e669c7ee967dbf7aad5ef73bbc585e557 + - path: data/jackhmmer_split/bfd-first_non_consensus_sequences.fasta-00000-of-00064 + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/jackhmmer_split/bfd-first_non_consensus_sequences.fasta-00000-of-00064 + size_bytes: 287578911 + sha256: 84648ea536e91a460fb8b18974f1daed003788bcdf6662a11bb68d2d07af7195 + - path: data/public_databases/pdb_seqres_2022_09_28.fasta + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/alphafold3/public_databases/pdb_seqres_2022_09_28.fasta + size_bytes: 232899463 + sha256: 1b3bc853322c32f2eea818065b8f569a18d25a52326a8d2c2c3de85752e55fe1 diff --git a/metadata/upload_layout_notes.md b/metadata/upload_layout_notes.md new file mode 100644 index 0000000000000000000000000000000000000000..ddbeeb19314cd6ec3f57fd9221cd10d591a70553 --- /dev/null +++ b/metadata/upload_layout_notes.md @@ -0,0 +1,18 @@ +# Upload layout notes + +This upload view is built from `dataset/bio_AlphaFold3_dataset` for ModelScope upload. + +The full local source contains `public_databases/mmcif_files/` with about 195k files, which exceeds the ModelScope upload pre-check file-count limit. The upload view therefore does not include that expanded directory. It includes the upstream archive instead: + +```text +data/public_databases/pdb_2022_09_28_mmcif_files.tar +``` + +Before running AlphaFold3 template search that requires `public_databases/mmcif_files`, extract the archive inside the dataset package: + +```bash +cd data/public_databases +tar -xf pdb_2022_09_28_mmcif_files.tar +``` + +Other database directories are kept as linked source directories in the upload view. diff --git a/onescience_run_manifest.yaml b/onescience_run_manifest.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d5ce068302e569f2fae9644ec5128a2ba0b3c75d --- /dev/null +++ b/onescience_run_manifest.yaml @@ -0,0 +1,290 @@ +onescience_manifest_version: "0.1" +resource_type: dataset +resource: + id: OneScience/AlphaFold3_dataset + name: AlphaFold3_dataset + domain: bio + domain_tags: [bio, biosciences, protein_structure, msa_database] + task: alphafold3_inference_database + task_tags: [inference_input, msa_search, template_search, data_pipeline] + modalities: [protein_sequence, msa, template_database, alphafold3_json] + input_formats: [alphafold3_json, fasta, mmcif, mmseqs_db] + output_formats: [alphafold3_json] + summary: AlphaFold3 运行所需的数据集资源，包含推理输入样例、公共数据库、MMseqs 数据库、Jackhmmer 分片数据库和对齐相关目录。 + +platform_resource: + primary: + platform: modelscope + repo_id: OneScience/AlphaFold3_dataset + repo_type: dataset + url: https://modelscope.cn/datasets/OneScience/AlphaFold3_dataset + revision: main + readme_path: README.md + manifest_path: manifest.yaml + mirrors: [] + access: + visibility: public + license: follows upstream database and AlphaFold3 data licenses + +website_integration: + enabled: true + click_target: + platform: modelscope + resource_url: https://modelscope.cn/datasets/OneScience/AlphaFold3_dataset + llm_handoff: + readme_required: true + manifest_required: true + download_readme_first: true + resolve_related_models: true + default_run_goal: dataset_validation + cwd_after_download: 下载后切换到数据集包根目录再运行验证命令；如果使用 --cache_dir，cwd 应为实际下载出的 OneScience/AlphaFold3_dataset 包根目录。 + +runtime: + enabled: true + onescience_domain: bio + min_onescience_version: null + supported_execution: [local, local_slurm, remote_slurm, scnet_mcp] + +onescience: + repo: https://gitee.com/onescience-ai/onescience + official_links: + gitee: + doc: https://gitee.com/onescience-ai/onescience-doc + onescience: https://gitee.com/onescience-ai/onescience + skills: https://gitee.com/onescience-ai/oneskills + github: + doc: https://github.com/onescience-ai/OneScience-doc + onescience: https://github.com/onescience-ai/OneScience + skills: https://github.com/onescience-ai/oneskills + install: + required_by_default: false + command: bash install.sh bio + source_paths: [] + compatibility: + examples_path: examples/biosciences/alphafold3 + status: examples_compatible + +runtime_package: + kind: standard_runtime_package + package_root: . + standard_layout: + workdir: . + config_dir: metadata + checkpoint_dir: null + data_dir: data + output_dir: outputs + apply_policy: + mode: direct_use + target: session_workdir + overwrite: true + protect_installed_onescience: true + entry_files: + - metadata/file_manifest.yaml + - scripts/validate_dataset.py + entrypoints: + preflight: scripts/validate_dataset.py + inference: null + train: null + finetune: null + evaluate: null + visualize: null + deploy: null + +files: + model_files: [] + dataset_files: + - id: infer_input_data + path: data/infer_input_data/ + role: inference_input + format: alphafold3_json + description_zh: AlphaFold3 JSON 推理输入样例，包含 all_data 和 pressure_data 子目录。 + required: true + required_for: [preflight, minimal_inference] + source: + platform: modelscope + repo_id: OneScience/AlphaFold3_dataset + repo_type: dataset + path: data/infer_input_data/ + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: data/infer_input_data/ + integrity_manifest: metadata/file_manifest.yaml + - id: public_databases + path: data/public_databases/ + role: database + format: fasta_mmcif + description_zh: Jackhmmer 和模板搜索所需公共数据库，包括 BFD、MGnify、UniRef90、UniProt、RNA、PDB seqres；上传视图用 pdb_2022_09_28_mmcif_files.tar 提供 mmCIF 文件，运行模板搜索前需解包为 mmcif_files 目录。 + required: true + required_for: [data_pipeline, jackhmmer_search] + local_path: data/public_databases/ + integrity_manifest: metadata/file_manifest.yaml + - id: mmseqs_db + path: data/mmseqsDB/ + role: database + format: mmseqs_db + description_zh: MMseqs 搜索所需数据库，包含 small_bfd、mgnify、uniprot_cluster_annot 和 uniref90 数据库。 + required: true + required_for: [mmseqs_search] + local_path: data/mmseqsDB/ + integrity_manifest: metadata/file_manifest.yaml + - id: jackhmmer_split + path: data/jackhmmer_split/ + role: database + format: sharded_fasta + description_zh: Jackhmmer 搜索用分片 FASTA 数据库。 + required: true + required_for: [jackhmmer_search] + local_path: data/jackhmmer_split/ + integrity_manifest: metadata/file_manifest.yaml + - id: align_db + path: data/alignDB/ + role: database + format: fasta + description_zh: 对齐相关数据库目录。 + required: false + required_for: [advanced_pipeline] + local_path: data/alignDB/ + config_files: + - id: file_manifest + path: metadata/file_manifest.yaml + role: integrity_manifest + description_zh: 记录整理后链接数据与原始数据之间的文件名、大小和 SHA256 校验信息。 + required: true + required_for: [preflight] + sample_files: + - id: sample_7r6r + path: data/infer_input_data/all_data/7r6r_data.json + role: inference_input + description_zh: 带 MSA 的最小推理样例。 + required: true + required_for: [dataset_validation, minimal_inference] + script_files: + - id: validate_dataset + path: scripts/validate_dataset.py + role: preflight + description_zh: 检查数据目录、样例 JSON 可读性、关键文件名、大小和 SHA256。 + required: true + required_for: [preflight] + +dataset: + format: [alphafold3_json, fasta, mmcif, mmseqs_db, sharded_fasta] + sample_unit: 一个 AlphaFold3 JSON fold input 或一个搜索数据库分片。 + schema: + path: metadata/file_manifest.yaml + json_required_fields: [dialect, version, name, sequences] + splits: + inference_all_data: data/infer_input_data/all_data/ + inference_pressure_data: data/infer_input_data/pressure_data/ + public_databases: data/public_databases/ + mmseqs: data/mmseqsDB/ + jackhmmer_split: data/jackhmmer_split/ + +relations: + required_datasets: [] + optional_datasets: [] + compatible_models: + - id: OneScience/AlphaFold3/ + role: inference_input_and_database + required_for: [preflight, inference, data_pipeline, msa_search] + resource_ref: + platform: modelscope + repo_id: OneScience/AlphaFold3/ + repo_type: model + url: https://modelscope.cn/models/OneScience/AlphaFold3/ + revision: main + readme_path: README.md + manifest_path: manifest.yaml + expected_local_path: data/alphafold3_dataset + adapter: null + +run_matrix: + scenarios: + - name: dataset_validation + default: true + goal: minimal_validation + capability: preflight + required_model_files: [] + required_dataset_files: [infer_input_data, public_databases, mmseqs_db, jackhmmer_split] + required_config_files: [file_manifest] + required_datasets: [] + command_refs: [commands.preflight.validate_dataset] + outputs: [dataset_validation_stdout] + prerequisites: + - cwd 为数据集包根目录。 + - name: provide_data_to_alphafold3_model + capability: data_pipeline + required_model_files: [] + required_dataset_files: [infer_input_data, public_databases, mmseqs_db, jackhmmer_split] + required_config_files: [file_manifest] + required_datasets: [] + command_refs: [commands.prepare.link_into_model_package] + outputs: [model_expected_dataset_path] + prerequisites: + - 已下载 OneScience/AlphaFold3/ 模型包。 + +capabilities: + inference: false + train: false + finetune: false + evaluate: false + visualize: false + deploy: false + preflight: true + data_pipeline: true + +commands: + download: + - name: download_dataset + cwd: . + command: "modelscope download --dataset OneScience/AlphaFold3_dataset" + description_zh: 下载 AlphaFold3 数据集标准仓库。 + - name: download_model + cwd: . + command: "modelscope download --model OneScience/AlphaFold3/" + description_zh: 下载适配模型仓库。 + prepare: + - name: link_into_model_package + cwd: . + command: "mkdir -p /path/to/model_package/data && ln -s $(pwd)/data /path/to/model_package/data/alphafold3_dataset" + description_zh: 将数据集包的 data 子目录链接到模型包期望的数据路径。 + preflight: + - name: validate_dataset + cwd: . + command: "python scripts/validate_dataset.py --root ." + description_zh: 验证数据目录、JSON 样例和关键文件完整性。 + inference: [] + train: [] + finetune: [] + evaluate: [] + visualize: [] + deploy: [] + +expected_outputs: + - id: dataset_validation_stdout + path: stdout + description_zh: "输出 dataset_validation_ok: true。" + - id: model_expected_dataset_path + path: /path/to/model_package/data/alphafold3_dataset + description_zh: 模型包可通过该路径访问数据集。 + +diagnostics: + - symptom: dataset_id_mismatch + cause_zh: README、manifest 或下载命令中的数据集 ID 与 OneScience/AlphaFold3_dataset 不一致。 + action_zh: 统一改为 OneScience/AlphaFold3_dataset。 + - symptom: missing_infer_input_data + cause_zh: 数据集目录未完整下载或 cwd 不在数据集包根目录。 + action_zh: 重新执行 modelscope download --dataset OneScience/AlphaFold3_dataset 并切换到下载后的数据集包根目录。 + - symptom: sha256_mismatch + cause_zh: 整理后的链接或复制文件与原始数据不一致。 + action_zh: 对照 metadata/file_manifest.yaml 的 source_path 重新整理对应文件。 + - symptom: mmseqs_database_missing + cause_zh: data/mmseqsDB 下缺少 small_bfd_db、mgnify_db、uniprot_cluster_annot_db 或 uniref90_db。 + action_zh: 检查数据集下载是否完整，或重新建立指向原始 mmseqsDB 的链接。 + +domain_extension: + bio: + molecule_types: [protein, rna, dna, ligand] + database_roles: [msa_search, template_search] + supported_search_backends: [mmseqs, jackhmmer] + json_schema_required_fields: [dialect, version, name, sequences] diff --git a/scripts/validate_dataset.py b/scripts/validate_dataset.py new file mode 100644 index 0000000000000000000000000000000000000000..7a35f22da5b9bf119e238b31edb51a3981ecc68f --- /dev/null +++ b/scripts/validate_dataset.py @@ -0,0 +1,62 @@ +#!/usr/bin/env python3 +from __future__ import annotations + +import argparse +import hashlib +import json +from pathlib import Path + +try: + import yaml +except ImportError as exc: + raise SystemExit("PyYAML is required for dataset validation: pip install pyyaml") from exc + + +def sha256(path: Path) -> str: + h = hashlib.sha256() + with path.open("rb") as f: + for chunk in iter(lambda: f.read(1024 * 1024), b""): + h.update(chunk) + return h.hexdigest() + + +def check_json(path: Path) -> None: + data = json.loads(path.read_text(encoding="utf-8")) + if data.get("dialect") != "alphafold3": + raise AssertionError(f"{path} dialect is not alphafold3") + if "sequences" not in data or not data["sequences"]: + raise AssertionError(f"{path} has no sequences") + + +def main() -> None: + parser = argparse.ArgumentParser() + parser.add_argument("--root", default=".") + parser.add_argument("--skip-hash", action="store_true") + args = parser.parse_args() + + root = Path(args.root).resolve() + manifest = yaml.safe_load((root / "metadata" / "file_manifest.yaml").read_text(encoding="utf-8")) + + for entry in manifest["dataset_directories"]: + path = root / entry["path"] + if not path.exists(): + raise AssertionError(f"missing linked dataset directory: {entry['path']}") + + for entry in manifest["files"]: + path = root / entry["path"] + if not path.is_file(): + raise AssertionError(f"missing verified data file: {entry['path']}") + if path.name != Path(entry["source_path"]).name: + raise AssertionError(f"filename mismatch: {entry['path']}") + if path.stat().st_size != entry["size_bytes"]: + raise AssertionError(f"size mismatch: {entry['path']}") + if not args.skip_hash and sha256(path) != entry["sha256"]: + raise AssertionError(f"sha256 mismatch: {entry['path']}") + + check_json(root / "data" / "infer_input_data" / "all_data" / "7r6r_data.json") + check_json(root / "data" / "infer_input_data" / "all_data" / "t1119_data.json") + print("dataset_validation_ok: true") + + +if __name__ == "__main__": + main()