Merge b6a4370 into b1fbcd9

NIPTool/API/external/api/api_v1/endpoints/login.py

@@ -42,7 +42,6 @@ def login(token: Token = Depends(login_for_access_token)):
             "Authorization": f"{token.get('token_type')} {token.get('access_token')}",
             "accept": "application/json",
         }
-        print(headers)
     return RedirectResponse("../batches", headers=headers)
 
 

NIPTool/API/external/api/api_v1/endpoints/sample.py

@@ -14,8 +14,30 @@
 @router.get("/samples/{sample_id}/")
 def sample(request: Request, sample_id: str, adapter: NiptAdapter = Depends(get_nipt_adapter)):
     """Sample view with sample information."""
+
     sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
-    batch = find.batch(batch_id=sample.get("batch_id"), adapter=adapter)
+    batch: Batch = find.batch(batch_id=sample.get("batch_id"), adapter=adapter)
+
+    return templates.TemplateResponse(
+        "sample/sample.html",
+        context=dict(
+            request=request,
+            current_user=User(username="mayapapaya", email="mayabrandi@123.com", role="RW"),
+            chrom_abnorm=CHROM_ABNORM,
+            sample=sample,
+            status_classes=STATUS_CLASSES,
+            batch=batch,
+            page_id="sample",
+        ),
+    )
+
+
+@router.post("/samples/{sample_id}/")
+def sample(request: Request, sample_id: str, adapter: NiptAdapter = Depends(get_nipt_adapter)):
+    """Sample view with sample information."""
+
+    sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
+    batch: Batch = find.batch(batch_id=sample.get("batch_id"), adapter=adapter)
 
     return templates.TemplateResponse(
         "sample/sample.html",

NIPTool/API/external/api/api_v1/endpoints/update.py

@@ -1,11 +1,12 @@
 import logging
 from typing import Iterable
-from typing import Optional
 
 from fastapi import APIRouter, Depends, Request
 from fastapi.responses import RedirectResponse
+from starlette.datastructures import FormData
+
 from NIPTool.adapter.plugin import NiptAdapter
-from NIPTool.crud import find, update
+from NIPTool.crud import update
 
 from NIPTool.models.database import User
 from NIPTool.API.external.utils import *
@@ -16,89 +17,105 @@
 
 LOG = logging.getLogger(__name__)
 
-from pydantic import BaseModel
+USER = User(username="mayapapaya", email="mayapapaya@mail.com", role="RW")
+
+
+@router.post("/set_sample_status")
+async def set_sample_status(request: Request, adapter: NiptAdapter = Depends(get_nipt_adapter)):
+    """Update the manualy interpreted chromosome abnormality status for a sample."""
+
+    form = await request.form()
+
+    if USER.role != "RW":
+        return RedirectResponse(request.headers.get("referer"))
+
+    sample_id: str = form["sample_id"]
+    sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
+
+    for abnormality in CHROM_ABNORM:
+        new_abnormality_status: str = form[abnormality]
+        abnormality_key: str = f"status_{abnormality}"
+        if sample.get(abnormality_key) == new_abnormality_status:
+            continue
+
+        LOG.debug(
+            "Updating %s to %s for sample %s",
+            abnormality_key,
+            new_abnormality_status,
+            sample_id,
+        )
+        time_stamp: str = datetime.now().strftime("%Y/%m/%d %H:%M:%S")
+        sample[abnormality_key] = new_abnormality_status
+        sample[f"status_change_{abnormality}"] = f"{USER.username} {time_stamp}"
+
+    update.sample(adapter=adapter, sample=Sample(**sample))
+    return RedirectResponse(request.headers.get("referer"))
+
 
+@router.post("/sample_comment")
+async def sample_comment(request: Request, adapter: NiptAdapter = Depends(get_nipt_adapter)):
+    """Update sample comment"""
 
-class Item(BaseModel):
-    form_id: str
-    sample_id: Optional[str]
+    form = await request.form()
 
+    if USER.role != "RW":
+        return RedirectResponse(request.headers.get("referer"))
 
-@router.post("/update_debugging")
-def update_debugging(
-    request: Request, item: Item, adapter: NiptAdapter = Depends(get_nipt_adapter)
-):
-    """Update the database"""
-    print(item)
-    print("hej")
-    time_stamp = datetime.now().strftime("%Y/%m/%d %H:%M:%S")
-    user = User(username="mayapapaya", email="mayabrandi@123.com", role="RW")
-    if user.role != "RW":
-        return "", 201
+    sample_id: str = form["sample_id"]
+    sample: Sample = find.sample(sample_id=sample_id, adapter=adapter)
+    comment: str = form.get("comment")
+    if comment != sample.comment:
+        sample.comment = comment
+        update.sample(adapter=adapter, sample=sample)
 
-    return RedirectResponse("batches/342712/")
+    return RedirectResponse(request.headers.get("referer"))
 
 
-@router.post("/update")
-def update(request: Request, adapter: NiptAdapter = Depends(get_nipt_adapter)):
-    """Update the database"""
+@router.post("/include_samples")
+async def include_samples(request: Request, adapter: NiptAdapter = Depends(get_nipt_adapter)):
+    """Update include status and comment for samples in batch"""
+
+    form = await request.form()
+
+    if USER.role != "RW":
+        return RedirectResponse(request.headers.get("referer"))
+
+    button_id = form.get("button_id")
+    samples: Iterable[str] = form.getlist("samples")
+    if button_id == "include all samples":
+        include_all_samples(samples=samples, adapter=adapter)
+    elif button_id == "Save":
+        save_samples(samples=samples, form=form, adapter=adapter)
+
+    return RedirectResponse(request.headers.get("referer"))
+
+
+def save_samples(samples: Iterable[str], form: FormData, adapter: NiptAdapter):
+    """Function to update sample.comment and sample.include."""
 
     time_stamp: str = datetime.now().strftime("%Y/%m/%d %H:%M:%S")
-    user = User(username="mayapapaya", email="mayapapaya@mail.com", role="RW")
-
-    if user.role != "RW":
-        return "", 201
-
-    if request.form.get("form_id") == "set_sample_status":
-        sample_id: str = request.form["sample_id"]
-        sample: Sample = find.sample(sample_id=sample_id)
-        # Convert to dict to fetch statuses
-        sample_dict: dict = sample.dict()
-        for abnormality in CHROM_ABNORM:
-            new_abnormality_status: str = request.form[abnormality]
-            abnormality_key: str = "_".join(["status", abnormality])
-            if sample_dict.get(abnormality_key) != new_abnormality_status:
-                LOG.debug(
-                    "Updating %s to %s for sample %s",
-                    abnormality_key,
-                    new_abnormality_status,
-                    sample_id,
-                )
-                sample[abnormality_key] = new_abnormality_status
-                sample["status_change_abnormality"] = " ".join([user.name, time_stamp])
-        update.sample(adapter=adapter, sample_object=Sample(**sample_dict))
-
-    if request.form.get("form_id") == "set_sample_comment" and request.form.get("comment"):
-        sample_id: str = request.form["sample_id"]
-        sample: Sample = find.sample(sample_id=sample_id)
-        comment: str = request.form.get("comment")
+    for sample_id in samples:
+        sample: Sample = find.sample(sample_id=sample_id, adapter=adapter)
+        comment: str = form.get(f"comment_{sample_id}")
+        include: bool = form.get(f"include_{sample_id}")
         if comment != sample.comment:
             sample.comment = comment
-        update.sample(adapter=adapter, sample_object=sample)
-
-    if request.form.get("button_id") == "Save":
-        samples: Iterable[str] = request.form.getlist("samples")
-        for sample_id in samples:
-            sample: Sample = find.sample(sample_id=sample_id)
-            comment: str = request.form.get(f"comment_{sample_id}")
-            include: bool = request.form.get(f"include_{sample_id}")
-            if comment != sample.comment:
-                sample.comment = comment
-            if include and not sample.include:
-                sample.include = True
-                sample.change_include_date = " ".join([user.name, time_stamp])
-            elif not include and sample.include:
-                sample.include = False
-            update.sample(adapter=adapter, sample_object=sample)
-
-    if request.form.get("button_id") == "include all samples":
-        samples: Iterable[str] = request.form.getlist("samples")
-        for sample_id in samples:
-            sample: Sample = find.sample(sample_id=sample_id)
-            if sample.include:
-                continue
+        if include and not sample.include:
             sample.include = True
-            sample.change_include_date = " ".join([user.name, time_stamp])
-            update.sample(adapter=adapter, sample_object=sample)
+            sample.change_include_date = f"{USER.username} {time_stamp}"
+        elif not include and sample.include:
+            sample.include = False
+        update.sample(adapter=adapter, sample=sample)
+
 
-    return RedirectResponse(request.url)
+def include_all_samples(samples: Iterable[str], adapter: NiptAdapter):
+    """Function to set sample.include=True for all samples."""
+
+    time_stamp: str = datetime.now().strftime("%Y/%m/%d %H:%M:%S")
+    for sample_id in samples:
+        sample: Sample = find.sample(sample_id=sample_id, adapter=adapter)
+        if sample.include:
+            continue
+        sample.include = True
+        sample.change_include_date = f"{USER.username} {time_stamp}"
+        update.sample(adapter=adapter, sample=sample)

NIPTool/API/external/api/api_v1/templates/batch/tabs/table.html

@@ -11,7 +11,7 @@
             <div class="col-lg-16">
                 <div class="panel panel-default">
                     <div class="panel-body">
-                        <form action="{{ url_for('update') }}" method="post">
+                        <form action="{{ url_for('include_samples') }}" method="post">
                             <input type=text name="form_id" value="include_samples" hidden>
                         <table>
                             <tbody>

NIPTool/API/external/api/api_v1/templates/sample/header.html

@@ -1,6 +1,6 @@
 {% block content %}
 
-<form action="{{ url_for('update') }}" method="post">
+<form action="{{ url_for('sample_comment') }}" method="post">
     <div class="vertical-center">
         <div class="row">
             <div class="col-lg-12">

NIPTool/API/external/api/api_v1/templates/sample/sample.html

@@ -16,7 +16,7 @@
                         <!-- /.panel-heading -->
                         <div class="panel-body">
                             <div class="table-responsive">
-                                <form action="{{ url_for('update') }}" method="post">
+                                <form action="{{ url_for('set_sample_status') }}" method="post">
                                     <input type=text name="form_id" value="set_sample_status" hidden>
                                     <input type=text name="sample_id" value="{{sample.sample_id}}" hidden>
                                     <table class="table table-bordered table-hover" >

NIPTool/API/external/constants.py

@@ -7,8 +7,8 @@
     "Other": "warning",
     "Failed": "danger",
 }
-CHROM_ABNORM = ["T13", "T18", "T21", "X0", "XXX", "XXY", "XYY"]
-TRIS_CHROM_ABNORM = ["T13", "T18", "T21"]
+CHROM_ABNORM = ["13", "18", "21", "X0", "XXX", "XXY", "XYY"]
+TRIS_CHROM_ABNORM = ["13", "18", "21"]
 SEX_CHROM_ABNORM = ["X0", "XXX", "XXY", "XYY"]
 STATUS_COLORS = {
     "Suspected": "#DBA901",

NIPTool/crud/update.py

@@ -12,5 +12,5 @@ def sample(adapter: NiptAdapter, sample: Sample) -> dict:
     sample_dict: dict = sample.dict(exclude_none=True)
     sample_id = sample.sample_id
     LOG.info("Updating sample %s", sample_id)
-    adapter.sample_collection.update_one({"sample_id": sample_id}, sample_dict)
+    adapter.sample_collection.update_one({"sample_id": sample_id}, {"$set": sample_dict})
     return sample_dict

NIPTool/models/database/sample.py

@@ -77,22 +77,22 @@ class Sample(BaseModel):
     CNVSegment: Optional[str]
     segmental_calls: Optional[str]
     include: Optional[bool]
-    change_include_date: Optional[str]
-    comment: Optional[str]
+    change_include_date: Optional[str] = ""
+    comment: Optional[str] = ""
     status_13: Optional[str]
     status_18: Optional[str]
     status_21: Optional[str]
     status_X0: Optional[str]
     status_XXX: Optional[str]
     status_XXY: Optional[str]
     status_XYY: Optional[str]
-    status_change_T13: Optional[str]
-    status_change_T18: Optional[str]
-    status_change_T21: Optional[str]
-    status_change_TX0: Optional[str]
-    status_change_TXXX: Optional[str]
-    status_change_TXXY: Optional[str]
-    status_change_TXYY: Optional[str]
+    status_change_13: Optional[str] = ""
+    status_change_18: Optional[str] = ""
+    status_change_21: Optional[str] = ""
+    status_change_X0: Optional[str] = ""
+    status_change_XXX: Optional[str] = ""
+    status_change_XXY: Optional[str] = ""
+    status_change_XYY: Optional[str] = ""
 
     class Config:
         allow_population_by_field_name = True