lingyuzeng/bttoxin-pipeline
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

chore: 初始版本提交 - 简化架构 + 轮询改造

Browse Source 
- 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>
This commit is contained in:
zly
2026-01-13 16:50:09 +08:00
parent 4c9a7d0978
commit fe353fc0bc
134 changed files with 1237947 additions and 2518 deletions
Download Patch File Download Diff File Expand all files Collapse all files

73870
tests/test_data/test2/ncbi_dataset/data/GCA_000338755.1/GCA_000338755.1_ASM33875v1_genomic.fna Normal file
View File

File diff suppressed because it is too large Load Diff

2
tests/test_data/test2/ncbi_dataset/data/assembly_data_report.jsonl Normal file
View File

@@ -0,0 +1,2 @@
{"assemblyInfo":{"assemblyLevel":"Complete Genome","assemblyName":"ASM33875v1","assemblyType":"haploid","submitter":"Institute of Plant Protection, Chinese Academy of Agricultural Sciences","bioprojectLineage":[{"bioprojects":[{"accession":"PRJNA185468","title":"Bacillus thuringiensis serovar kurstaki str. HD73 Genome sequencing"}]}],"sequencingTech":"Sanger dideoxy sequencing; 454; Illumina","biosample":{"accession":"SAMN02603412","lastUpdated":"2017-12-19T20:54:18.153","publicationDate":"2014-01-30T14:21:27.853","submissionDate":"2014-01-30T14:21:27.853","sampleIds":[{"label":"Sample name","value":"CP004069"},{"db":"SRA","value":"SRS2771020"}],"description":{"title":"Sample from Bacillus thuringiensis serovar kurstaki str. HD73","organism":{"taxId":1279365,"organismName":"Bacillus thuringiensis serovar kurstaki str. HD73"}},"owner":{"name":"NCBI"},"models":["Generic"],"bioprojects":[{"accession":"PRJNA185468"}],"package":"Generic.1.0","attributes":[{"name":"strain","value":"HD73"},{"name":"serovar","value":"kurstaki"}],"status":{"status":"live","when":"2014-01-30T14:21:27.853"},"serovar":"kurstaki","strain":"HD73"},"comments":"The bacteria is available from Fuping Song (fpsong@ippcaas.cn)","assemblyStatus":"current","pairedAssembly":{"accession":"GCF_000338755.1","status":"current","annotationName":"GCF_000338755.1-RS_2025_04_14"},"bioprojectAccession":"PRJNA185468","assemblyMethod":"newbler v. 2.3","releaseDate":"2013-02-08"},"assemblyStats":{"totalNumberOfChromosomes":8,"totalSequenceLength":"5908575","totalUngappedLength":"5908575","numberOfContigs":8,"contigN50":5646799,"contigL50":1,"numberOfScaffolds":8,"scaffoldN50":5646799,"scaffoldL50":1,"numberOfComponentSequences":8,"gcCount":"2077976","gcPercent":35,"atgcCount":"5908575"},"annotationInfo":{"name":"Annotation submitted by Institute of Plant Protection, Chinese Academy of Agricultural Sciences","provider":"Institute of Plant Protection, Chinese Academy of Agricultural Sciences","releaseDate":"2017-08-22","stats":{"geneCounts":{"total":6334,"proteinCoding":6194,"nonCoding":140}}},"currentAccession":"GCA_000338755.1","checkmInfo":{"checkmMarkerSet":"Bacillus thuringiensis","checkmMarkerSetRank":"species","checkmVersion":"v1.2.3","completeness":96.36,"contamination":0.92,"completenessPercentile":12.3817,"checkmSpeciesTaxId":1428},"averageNucleotideIdentity":{"taxonomyCheckStatus":"OK","matchStatus":"synonym_match","submittedOrganism":"Bacillus thuringiensis serovar kurstaki str. HD73","submittedSpecies":"Bacillus thuringiensis","category":"category_na","submittedAniMatch":{"assembly":"GCA_002243685.1","organismName":"Bacillus thuringiensis","category":"suspected_type","ani":96.35,"assemblyCoverage":83.17,"typeAssemblyCoverage":76.23},"bestAniMatch":{"assembly":"GCA_046524075.1","organismName":"Bacillus cereus","category":"type","ani":97.19,"assemblyCoverage":79.94,"typeAssemblyCoverage":86.65},"comment":"na"},"accession":"GCA_000338755.1","pairedAccession":"GCF_000338755.1","sourceDatabase":"SOURCE_DATABASE_GENBANK","organism":{"taxId":1279365,"organismName":"Bacillus thuringiensis serovar kurstaki str. HD73","infraspecificNames":{"strain":"HD73"}}}
{"assemblyInfo":{"assemblyLevel":"Complete Genome","assemblyName":"ASM33875v1","assemblyType":"haploid","submitter":"Institute of Plant Protection, Chinese Academy of Agricultural Sciences","bioprojectLineage":[{"bioprojects":[{"accession":"PRJNA185468","title":"Bacillus thuringiensis serovar kurstaki str. HD73 Genome sequencing"}]}],"sequencingTech":"Sanger dideoxy sequencing; 454; Illumina","biosample":{"accession":"SAMN02603412","lastUpdated":"2017-12-19T20:54:18.153","publicationDate":"2014-01-30T14:21:27.853","submissionDate":"2014-01-30T14:21:27.853","sampleIds":[{"label":"Sample name","value":"CP004069"},{"db":"SRA","value":"SRS2771020"}],"description":{"title":"Sample from Bacillus thuringiensis serovar kurstaki str. HD73","organism":{"taxId":1279365,"organismName":"Bacillus thuringiensis serovar kurstaki str. HD73"}},"owner":{"name":"NCBI"},"models":["Generic"],"bioprojects":[{"accession":"PRJNA185468"}],"package":"Generic.1.0","attributes":[{"name":"strain","value":"HD73"},{"name":"serovar","value":"kurstaki"}],"status":{"status":"live","when":"2014-01-30T14:21:27.853"},"serovar":"kurstaki","strain":"HD73"},"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/\nThe bacteria is available from Fuping Song (fpsong@ippcaas.cn)","assemblyStatus":"current","pairedAssembly":{"accession":"GCA_000338755.1","status":"current","annotationName":"Annotation submitted by Institute of Plant Protection, Chinese Academy of Agricultural Sciences"},"bioprojectAccession":"PRJNA185468","assemblyMethod":"newbler v. 2.3","releaseDate":"2013-02-08"},"assemblyStats":{"totalNumberOfChromosomes":8,"totalSequenceLength":"5908575","totalUngappedLength":"5908575","numberOfContigs":8,"contigN50":5646799,"contigL50":1,"numberOfScaffolds":8,"scaffoldN50":5646799,"scaffoldL50":1,"numberOfComponentSequences":8,"gcCount":"2077976","gcPercent":35,"atgcCount":"5908575"},"annotationInfo":{"name":"GCF_000338755.1-RS_2025_04_14","provider":"NCBI RefSeq","releaseDate":"2025-04-14","stats":{"geneCounts":{"total":6168,"proteinCoding":5679,"nonCoding":145,"pseudogene":344}},"method":"Best-placed reference protein set; GeneMarkS-2+","pipeline":"NCBI Prokaryotic Genome Annotation Pipeline (PGAP)","softwareVersion":"6.10"},"currentAccession":"GCF_000338755.1","checkmInfo":{"checkmMarkerSet":"Bacillus thuringiensis","checkmMarkerSetRank":"species","checkmVersion":"v1.2.3","completeness":96.36,"contamination":0.92,"completenessPercentile":12.3817,"checkmSpeciesTaxId":1428},"averageNucleotideIdentity":{"taxonomyCheckStatus":"OK","matchStatus":"synonym_match","submittedOrganism":"Bacillus thuringiensis serovar kurstaki str. HD73","submittedSpecies":"Bacillus thuringiensis","category":"category_na","submittedAniMatch":{"assembly":"GCA_002243685.1","organismName":"Bacillus thuringiensis","category":"suspected_type","ani":96.35,"assemblyCoverage":83.17,"typeAssemblyCoverage":76.23},"bestAniMatch":{"assembly":"GCA_046524075.1","organismName":"Bacillus cereus","category":"type","ani":97.19,"assemblyCoverage":79.94,"typeAssemblyCoverage":86.65},"comment":"na"},"accession":"GCF_000338755.1","pairedAccession":"GCA_000338755.1","sourceDatabase":"SOURCE_DATABASE_REFSEQ","organism":{"taxId":1279365,"organismName":"Bacillus thuringiensis serovar kurstaki str. HD73","infraspecificNames":{"strain":"HD73"}}}

3
tests/test_data/test2/ncbi_dataset/data/data_summary.tsv Normal file
View File

@@ -0,0 +1,3 @@
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
Bacillus thuringiensis serovar kurstaki str. HD73 strain: HD73 1279365 ASM33875v1 GCA_000338755.1 GenBank Annotation submitted by Institute of Plant Protection, Chinese Academy of Agricultural Sciences Complete Genome 5646799 5908575 2013-02-08 6334 PRJNA185468 SAMN02603412
Bacillus thuringiensis serovar kurstaki str. HD73 strain: HD73 1279365 ASM33875v1 GCF_000338755.1 RefSeq GCF_000338755.1-RS_2025_04_14 Complete Genome 5646799 5908575 2013-02-08 6168 PRJNA185468 SAMN02603412
1 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
2 Bacillus thuringiensis serovar kurstaki str. HD73 strain: HD73 1279365 ASM33875v1 GCA_000338755.1 GenBank Annotation submitted by Institute of Plant Protection, Chinese Academy of Agricultural Sciences Complete Genome 5646799 5908575 2013-02-08 6334 PRJNA185468 SAMN02603412
3 Bacillus thuringiensis serovar kurstaki str. HD73 strain: HD73 1279365 ASM33875v1 GCF_000338755.1 RefSeq GCF_000338755.1-RS_2025_04_14 Complete Genome 5646799 5908575 2013-02-08 6168 PRJNA185468 SAMN02603412

35
tests/test_data/test2/ncbi_dataset/data/dataset_catalog.json Normal file
View File

@@ -0,0 +1,35 @@
{
"apiVersion": "V2",
"assemblies": [
{
"files": [
{
"filePath": "data_summary.tsv",
"fileType": "DATA_TABLE",
"uncompressedLengthBytes": "686"
},
{
"filePath": "assembly_data_report.jsonl",
"fileType": "DATA_REPORT",
"uncompressedLengthBytes": "6616"
}
]
},{
"accession": "GCA_000338755.1",
"files": [
{
"filePath": "GCA_000338755.1/GCA_000338755.1_ASM33875v1_genomic.fna",
"fileType": "GENOMIC_NUCLEOTIDE_FASTA",
"uncompressedLengthBytes": "5983182"
}
]
},{
"accession": "GCF_000338755.1",
"files": [
{
"filePath": "GCF_000338755.1/GCF_000338755.1_ASM33875v1_genomic.fna",
"fileType": "GENOMIC_NUCLEOTIDE_FASTA",
"uncompressedLengthBytes": "5983192"
}
]
}]}