XspecT 0.4.1__py3-none-any.whl → 0.5.0__py3-none-any.whl

xspect/fastapi.py

@@ -1,102 +0,0 @@
-"""FastAPI application for XspecT."""
-
-from uuid import uuid4
-from pathlib import Path
-from shutil import copyfileobj
-from fastapi import FastAPI, UploadFile, BackgroundTasks
-from xspect.definitions import get_xspect_runs_path, get_xspect_upload_path
-from xspect.download_models import download_test_models
-from xspect.file_io import filter_sequences
-import xspect.model_management as mm
-from xspect.train import train_from_ncbi
-
-app = FastAPI()
-
-
-@app.get("/download-filters")
-def download_filters():
-    """Download filters."""
-    download_test_models("http://assets.adrianromberg.com/xspect-models.zip")
-
-
-@app.get("/classify")
-def classify(genus: str, file: str, meta: bool = False, step: int = 500):
-    """Classify uploaded sample."""
-
-    input_path = get_xspect_upload_path() / file
-
-    uuid = str(uuid4())
-
-    if meta:
-        genus_model = mm.get_genus_model(genus)
-        genus_result = genus_model.predict(input_path, step=step)
-        included_ids = genus_result.get_filtered_subsequence_labels(genus)
-        if not included_ids:
-            return {"message": "No sequences found for the given genus."}
-        filtered_path = get_xspect_runs_path() / f"filtered_{uuid}.fasta"
-        filter_sequences(
-            Path(input_path),
-            Path(filtered_path),
-            included_ids=included_ids,
-        )
-        input_path = filtered_path
-
-    species_model = mm.get_species_model(genus)
-    species_result = species_model.predict(input_path, step=step)
-    species_result.save(get_xspect_runs_path() / f"result_{uuid}.json")
-    return species_result.to_dict()
-
-
-@app.post("/train")
-def train(genus: str, background_tasks: BackgroundTasks, svm_steps: int = 1):
-    """Train NCBI model."""
-    background_tasks.add_task(train_from_ncbi, genus, svm_steps)
-
-    return {"message": "Training started."}
-
-
-@app.get("/list-models")
-def list_models():
-    """List available models."""
-    return mm.get_models()
-
-
-@app.get("/model-metadata")
-def get_model_metadata(model_slug: str):
-    """Get metadata of a model."""
-    return mm.get_model_metadata(model_slug)
-
-
-@app.post("/model-metadata")
-def post_model_metadata(model_slug: str, author: str, author_email: str):
-    """Update metadata of a model."""
-    try:
-        mm.update_model_metadata(model_slug, author, author_email)
-    except ValueError as e:
-        return {"error": str(e)}
-    return {"message": "Metadata updated."}
-
-
-@app.post("/model-display-name")
-def post_model_display_name(model_slug: str, filter_id: str, display_name: str):
-    """Update display name of a filter in a model."""
-    try:
-        mm.update_model_display_name(model_slug, filter_id, display_name)
-    except ValueError as e:
-        return {"error": str(e)}
-    return {"message": "Display name updated."}
-
-
-@app.post("/upload-file")
-def upload_file(file: UploadFile):
-    """Upload file to the server."""
-    upload_path = get_xspect_upload_path() / file.filename
-
-    if not upload_path.exists():
-        try:
-            with upload_path.open("wb") as buffer:
-                copyfileobj(file.file, buffer)
-        finally:
-            file.file.close()
-
-    return {"filename": file.filename}

xspect-0.4.1.dist-info/RECORD

@@ -1,24 +0,0 @@
-xspect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/definitions.py,sha256=fVn_li_s2hriOSGJ69o_H8H-vkw1znvkryhBj7WMnF4,1219
-xspect/download_models.py,sha256=y1wFJZa1xOJfvUP78zKkRs46O-WqKBL90vmo5AYUio0,853
-xspect/fastapi.py,sha256=DOef3MqWPdBmdYBo8Z9SPmWrbJHOsQxQe3GrC4f__Rc,3165
-xspect/file_io.py,sha256=YmfoKEQdHHEi8dO2G5Kt4tSNi5LuWW0VZ74pyYRHiTo,5937
-xspect/main.py,sha256=twIn48wPDFOEejQroYN8JM8a40naEqT_BUgrMAwwYck,12154
-xspect/model_management.py,sha256=UbmAr3YOZ4oy_9iVvApCLstYHGkcmneHEC_yftRIqCI,3010
-xspect/ncbi.py,sha256=sSJO3g8n89Qw6UJjAy13bpjOcIGSquTKNKVHNUMbDeM,10072
-xspect/train.py,sha256=7I7-inWGJe_VDzII9dLZ8U-8SUCZDIrhb-eNOZEyfss,10703
-xspect/mlst_feature/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/mlst_feature/mlst_helper.py,sha256=3zhhEomkk-qiObbQ82TM_YHuyVCJ7_XgyzsYM_4TS0E,5760
-xspect/mlst_feature/pub_mlst_handler.py,sha256=oss3CkJNt6041p3qnMdOfoX8ZgUfpB93CUim-Yakc9A,5031
-xspect/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/models/probabilistic_filter_mlst_model.py,sha256=JMc0yBJPo7J9b-GpvhDmzhwWPIKOwatAq0edDgM72PE,11735
-xspect/models/probabilistic_filter_model.py,sha256=l8mhcRgHPso7qIgI56buCnE3ZleO3gPWOZEpgrycOBA,10029
-xspect/models/probabilistic_filter_svm_model.py,sha256=xXimcv3iWnG1JiFyrk6UqkP9hFIxWGDdb__fRdQYwro,6245
-xspect/models/probabilistic_single_filter_model.py,sha256=yxWnCt4IP-3ZRLP4pRA3f2VTHc0_4g17PDCyOFayDDg,4090
-xspect/models/result.py,sha256=ELWiDlQPlxNG7ceLpth60Z_Hb1ZdopDJ3vgHBPgSRm8,3989
-xspect-0.4.1.dist-info/licenses/LICENSE,sha256=bhBGDKIRUVwYIHGOGO5hshzuVHyqFJajvSOA3XXOLKI,1094
-xspect-0.4.1.dist-info/METADATA,sha256=BLTAPyNGEjUxxFUqGvdgyFy8T0p9b8w8IOBbUBvnv28,4477
-xspect-0.4.1.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
-xspect-0.4.1.dist-info/entry_points.txt,sha256=L7qliX3pIuwupQxpuOSsrBJCSHYPOPNEzH8KZKQGGUw,43
-xspect-0.4.1.dist-info/top_level.txt,sha256=hdoa4cnBv6OVzpyhMmyxpJxEydH5n2lDciy8urc1paE,7
-xspect-0.4.1.dist-info/RECORD,,