chore: 初始版本提交 - 简化架构 + 轮询改造
- 移除 Motia Streams 实时通信，改用 3 秒轮询 - 简化前端代码，移除冗余组件 - 简化后端架构，准备 FastAPI 重构 - 更新 pixi.toml 环境配置 - 保留 bttoxin_digger_v5_repro 作为参考文档 Co-Authored-By: Claude <noreply@anthropic.com>
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{"assemblyInfo":{"assemblyLevel":"Complete Genome","assemblyName":"ASM344539v2","assemblyType":"haploid","submitter":"MICALIS INRA","bioprojectLineage":[{"bioprojects":[{"accession":"PRJNA303961","title":"Bacillus thuringiensis serovar israelensis strain AM65-52 and other related strains"}]}],"sequencingTech":"Illumina","biosample":{"accession":"SAMN04288432","lastUpdated":"2021-02-28T02:59:31.467","publicationDate":"2016-05-01T00:00:00.000","submissionDate":"2015-11-24T05:04:10.000","sampleIds":[{"label":"Sample name","value":"WNF19#1"},{"db":"SRA","value":"SRS4274306"}],"description":{"title":"strain AM65-52","organism":{"taxId":1430,"organismName":"Bacillus thuringiensis serovar israelensis"},"comment":"bacterial colony"},"owner":{"name":"MICALIS INRA","contacts":[{}]},"models":["Microbe, viral or environmental"],"package":"Microbe.1.0","attributes":[{"name":"strain","value":"AM65-52"},{"name":"host","value":"Vectobac"},{"name":"isolation_source","value":"Commercial powder"},{"name":"collection_date","value":"2014-06-20"},{"name":"geo_loc_name","value":"France"},{"name":"sample_type","value":"bacterial clone"},{"name":"altitude","value":"100 m"},{"name":"biomaterial_provider","value":"Micalis, INRA"},{"name":"collected_by","value":"Alexei Sorokin"},{"name":"genotype","value":"toxic against mosquito"},{"name":"identified_by","value":"Alexei Sorokin"},{"name":"lab_host","value":"Bacillus thuringiensis"},{"name":"passage_history","value":"direct colony from commertial powder"},{"name":"samp_size","value":"one kg"},{"name":"serovar","value":"serovar=H14"},{"name":"temp","value":"30C"},{"name":"component_organism","value":"Bacillus phage pGIL02"}],"status":{"status":"live","when":"2016-05-01T00:50:56.207"},"biomaterialProvider":"Micalis, INRA","collectedBy":"Alexei Sorokin","collectionDate":"2014-06-20","geoLocName":"France","host":"Vectobac","identifiedBy":"Alexei Sorokin","isolationSource":"Commercial powder","serovar":"serovar=H14","strain":"AM65-52"},"comments":"The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/","assemblyStatus":"current","pairedAssembly":{"accession":"GCA_003445395.2","status":"current","annotationName":"NCBI Prokaryotic Genome Annotation Pipeline (PGAP)","onlyGenbank":"chromosome ","refseqGenbankAreDifferent":true,"differences":"Removed chromosome "},"bioprojectAccession":"PRJNA303961","assemblyMethod":"SPAdes v. 3.5.0","releaseDate":"2016-11-29"},"assemblyStats":{"totalNumberOfChromosomes":9,"totalSequenceLength":"6700047","totalUngappedLength":"6700047","numberOfContigs":9,"contigN50":5499731,"contigL50":1,"numberOfScaffolds":9,"scaffoldN50":5499731,"scaffoldL50":1,"numberOfComponentSequences":9,"gcCount":"2343207","gcPercent":35,"genomeCoverage":"300","atgcCount":"6700047"},"annotationInfo":{"name":"GCF_003445395.2-RS_2025_03_19","provider":"NCBI RefSeq","releaseDate":"2025-03-19","stats":{"geneCounts":{"total":7000,"proteinCoding":6579,"nonCoding":179,"pseudogene":242}},"method":"Best-placed reference protein set; GeneMarkS-2+","pipeline":"NCBI Prokaryotic Genome Annotation Pipeline (PGAP)","softwareVersion":"6.9"},"currentAccession":"GCF_003445395.2","checkmInfo":{"checkmMarkerSet":"Bacillus thuringiensis","checkmMarkerSetRank":"species","checkmVersion":"v1.2.3","completeness":99.3,"contamination":0.74,"completenessPercentile":83.2006,"checkmSpeciesTaxId":1428},"averageNucleotideIdentity":{"taxonomyCheckStatus":"Inconclusive","matchStatus":"below_threshold_match","submittedOrganism":"Bacillus thuringiensis serovar israelensis","submittedSpecies":"Bacillus thuringiensis","category":"category_na","submittedAniMatch":{"assembly":"GCA_002243685.1","organismName":"Bacillus thuringiensis","category":"suspected_type","ani":96.5,"assemblyCoverage":72.97,"typeAssemblyCoverage":76.02},"bestAniMatch":{"assembly":"GCA_002243685.1","organismName":"Bacillus thuringiensis","category":"suspected_type","ani":96.5,"assemblyCoverage":72.97,"typeAssemblyCoverage":76.02},"comment":"na"},"accession":"GCF_003445395.2","pairedAccession":"GCA_003445395.2","sourceDatabase":"SOURCE_DATABASE_REFSEQ","organism":{"taxId":1430,"organismName":"Bacillus thuringiensis serovar israelensis","infraspecificNames":{"strain":"AM65-52"}}}
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tests/test_data/test1/ncbi_dataset/data/data_summary.tsv
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Organism Scientific Name Organism Common Name Organism Qualifier Taxonomy id Assembly Name Assembly Accession Source Annotation Level Contig N50 Size Submission Date Gene Count BioProject BioSample
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Bacillus thuringiensis serovar israelensis strain: AM65-52 1430 ASM344539v2 GCA_003445395.2 GenBank NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Complete Genome 5499731 6700047 2016-11-29 6950 PRJNA303961 SAMN04288432
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Bacillus thuringiensis serovar israelensis strain: AM65-52 1430 ASM344539v2 GCF_003445395.2 RefSeq GCF_003445395.2-RS_2025_03_19 Complete Genome 5499731 6700047 2016-11-29 7000 PRJNA303961 SAMN04288432
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tests/test_data/test1/ncbi_dataset/data/dataset_catalog.json
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