Merge pull request #4 from NBISweden/experimental/add-initial-annotat…

…ion-functionality

Experimental/add initial annotation functionality

.gitignore

@@ -1,2 +1,3 @@
 .DS_Store
-__pycache__/
+__pycache__/
+venv

Dockerfile

@@ -1,31 +1,12 @@
 # syntax=docker/dockerfile:1.4
-FROM python:3.9-slim as BUILDER
+FROM python:3.9-slim
 
 WORKDIR /app
 
-RUN apt-get update && \
-    apt-get -y install gcc mono-mcs && \
-    rm -rf /var/lib/apt/lists/*
-
 COPY requirements.txt /app
 RUN --mount=type=cache,target=/root/.cache/pip \
     pip3 install -r requirements.txt
 
 COPY . /app
 
-ENTRYPOINT ["python3"]
-CMD ["app.py"]
-
-FROM builder as dev-envs
-
-RUN <<EOF
-apk update
-apk add git
-EOF
-
-RUN <<EOF
-addgroup -S docker
-adduser -S --shell /bin/bash --ingroup docker vscode
-EOF
-# install Docker tools (cli, buildx, compose)
-COPY --from=gloursdocker/docker / /
+CMD ["flask", "--app", "app.py", "--debug", "run", "--host", "0.0.0.0"]

app.py

@@ -1,37 +1,86 @@
-from flask import Flask, request, render_template, Response
-from add import add
-from placeholder import VectorOligoSearch
+from flask import (
+    Flask,
+    request,
+    render_template,
+    Response,
+    json,
+    make_response,
+    jsonify
+)
+import io
+import csv
+import logging
+from itertools import chain
+from search.oligo_search import search, search_to_file
+from search.search import SearchError
 
+
+logger = logging.getLogger(__name__)
 app = Flask(__name__)
 
+
+
 @app.route('/')
-def hello():
-  return render_template('root.html')
+def root():
+    return render_template('root.html')
 
-@app.route('/form', methods=['POST', 'GET'])
-# Sample form POST to get input and render result
+
+@app.route('/search', methods=['POST', 'GET'])
 def form():
-    form_input = None
+    gene_ids = []
     output = None
+    error = None
+    status_code = 200
 
     if request.method == 'POST':
-        form_input = request.form['userInput']
-        output = VectorOligoSearch(form_input)
+        try:
+            gene_id = request.form['gene-id']
+            gene_list = request.form.get('gene-list', "").strip()
+            gene_ids = (
+                [gene_id] if len(gene_list) == 0
+                else [g.strip().rstrip('\r\n') for g in gene_list.split("\n")]
+            )
+            output = search(gene_ids)
+        except SearchError as e:
+            error = str(e)
+            status_code = 404
+
+    return render_template(
+      'form.html',
+      gene_ids=gene_ids,
+      output=output,
+      error=error,
+      status_code=status_code,
+    )
+
 
-    return render_template('form.html',
-      input=form_input,
-      output=output)
+@app.route('/oligo-search')
+def oligo_search():
+    gene_ids = request.args.getlist('gene-id')
+    try:
+        output = search(gene_ids)
+        return jsonify(output)
+    except SearchError as e:
+        error = str(e)
+        return make_response(jsonify({"error": error}), 404)
 
-# Sample download generated CSV
+    
 @app.route("/get")
-def getPlotCSV():
-    genome_id = request.args.get('id')
-    csv = VectorOligoSearch(genome_id)
+def get_data():
+    gene_ids = request.args.getlist('gene-id')
+    format = request.args.get('format', 'csv')
+    (output, ext) = search_to_file(
+        gene_ids,
+        output_format=format
+    )
     return Response(
-        csv,
+        output,
         mimetype="text/csv",
-        headers={"Content-disposition":
-                 f"attachment; filename={genome_id}.csv"})
+        headers={
+            "Content-disposition":
+                f"attachment; filename=oligo-sequences.{ext}"
+            }
+        )
 
 if __name__ == '__main__':
-  app.run(host='0.0.0.0', port=8000)
+    app.run(host='0.0.0.0', port=8000)

compose.yaml

@@ -2,9 +2,8 @@ services:
   web:
     build:
       context: .
-      target: builder
-    # flask requires SIGINT to stop gracefully
-    # (default stop signal from Compose is SIGTERM)
     stop_signal: SIGINT
     ports:
-      - '8000:8000'
+      - '127.0.0.1:5000:5000'
+    volumes:
+      - ./:/app

questions.md

@@ -0,0 +1,4 @@
+# Technical questions
+- How strictly do we want to stick to the original code?
+- Are there any restrictions on how much we can clean up the code?
+-