Merge pull request #29 from camicroscope/develop

3.7.2

Dockerfile

@@ -26,8 +26,8 @@ RUN pip3 install -r requirements.txt
 EXPOSE 4000
 
 #debug/dev only
-#ENV FLASK_APP SlideServer.py
-#CMD python -m flask run --host=0.0.0.0 --port=4000
+# ENV FLASK_APP SlideServer.py
+# CMD python -m flask run --host=0.0.0.0 --port=4000
 
 #prod only
 CMD gunicorn -w 4 -b 0.0.0.0:4000 SlideServer:app --timeout 400

SlideServer.py

@@ -6,12 +6,18 @@
 import string
 import sys
 import pyvips
+from os import listdir
+from os.path import isfile, join
 
+
+import urllib
 import flask
 import flask_cors
 import openslide
 from werkzeug.utils import secure_filename
 import dev_utils
+import requests
+
 
 try:
     from io import BytesIO
@@ -27,7 +33,7 @@
 app.config['TOKEN_SIZE'] = 10
 app.config['SECRET_KEY'] = os.urandom(24)
 
-ALLOWED_EXTENSIONS = set(['svs', 'tif', 'tiff', 'vms', 'vmu', 'ndpi', 'scn', 'mrxs', 'bif', 'svslide'])
+ALLOWED_EXTENSIONS = set(['svs', 'tif', 'tiff', 'vms', 'vmu', 'ndpi', 'scn', 'mrxs', 'bif', 'svslide'])    
 
 
 def allowed_file(filename):
@@ -130,6 +136,29 @@ def finish_upload(token):
     # get info associated with token
     # move the file out of temp to upload dir
 
+# Delete the requested slide
+@app.route('/slide/delete', methods=['POST'])
+def slide_delete():
+    body = flask.request.get_json()
+
+    if not body:
+        return flask.Response(json.dumps({"error": "Missing JSON body"}), status=400)
+
+    filename = body['filename']
+    if filename and allowed_file(filename):
+        filename = secure_filename(filename)
+        filepath = os.path.join(app.config['UPLOAD_FOLDER'], filename)
+        if os.path.isfile(filepath):
+            os.remove(os.path.join(app.config['UPLOAD_FOLDER'], filename))
+            return flask.Response(json.dumps({"deleted": filename, "success": True})) 
+        else:
+            return flask.Response(json.dumps({"error": "File with name '" + filename + "' does not exist"}), status=400)
+
+    else:
+        return flask.Response(json.dumps({"error": "Invalid filename"}), status=400)
+
+    # check for file if it exists or not
+    # delete the file
 
 @app.route("/test", methods=['GET'])
 def testRoute():
@@ -150,3 +179,49 @@ def singleThumb(filepath):
 @app.route("/data/many/<filepathlist>", methods=['GET'])
 def multiSlide(filepathlist):
     return json.dumps(dev_utils.getMetadataList(json.loads(filepathlist), app.config['UPLOAD_FOLDER']))
+
+
+@app.route("/getSlide/<image_name>")
+def getSlide(image_name):
+    if(os.path.isfile("/images/"+image_name)):
+        return flask.send_from_directory(app.config["UPLOAD_FOLDER"], filename=image_name, as_attachment=True)
+    else:
+        return flask.Response(json.dumps({"error": "File does not exist"}), status=404)
+
+# using the token from the start url upload endpoint
+@app.route('/urlupload/continue/<token>', methods=['POST'])
+def continue_urlfile(token):
+    token = secure_filename(token)
+    tmppath = os.path.join(app.config['TEMP_FOLDER'], token)
+    if os.path.isfile(tmppath):
+        body = flask.request.get_json()
+        if not body:
+            return flask.Response(json.dumps({"error": "Missing JSON body"}), status=400)
+        if not 'url' in body:
+            return flask.Response(json.dumps({"error": "File url not present in body"}), status=400)
+        else:
+            url = body['url']
+            try:
+                url = urllib.parse.unquote(url)
+                urllib.request.urlretrieve(url, tmppath)
+                return flask.Response(json.dumps({"status": "OK Uploaded"}), status=200)
+            except:
+                return flask.Response(json.dumps({"error": "URL invalid"}), status=400)
+    else:
+        return flask.Response(json.dumps({"error": "Token Not Recognised"}), status=400)
+
+# Route to check if the URL file has completely uploaded to the server 
+# Query Params: 'url', 'token'
+@app.route('/urlupload/check', methods=['GET'])
+def urlUploadStatus():
+    url = flask.request.args.get('url')
+    url = urllib.parse.unquote(url)
+    token = flask.request.args.get('token')
+    info = requests.head(url)
+    urlFileSize = int(info.headers['Content-Length'])
+    fileSize = os.path.getsize(app.config['TEMP_FOLDER']+'/'+token)
+    if(fileSize >= urlFileSize):
+        return flask.Response(json.dumps({"uploaded": "True"}), status=200)
+    else:
+        return flask.Response(json.dumps({"uploaded": "False"}), status=200)
+

dev_utils.py

@@ -34,8 +34,10 @@ def getMetadata(filename, upload_folder):
         "openslide.level[0].width", None)
     metadata['vendor'] = slideData.get(openslide.PROPERTY_NAME_VENDOR, None)
     metadata['level_count'] = int(slideData.get('level_count', 1))
-    metadata['objective'] = float(slideData.get("aperio.AppMag", -1.0))
+    metadata['objective'] = float(slideData.get(openslide.PROPERTY_NAME_OBJECTIVE_POWER, 0) or
+                                  slideData.get("aperio.AppMag", -1.0))
     metadata['md5sum'] = file_md5(filepath)
+    metadata['comment'] = slideData.get(openslide.PROPERTY_NAME_COMMENT, None)
     metadata['study'] = ""
     metadata['specimen'] = ""
     return metadata

requirements.txt

@@ -2,4 +2,4 @@ openslide-python
 flask
 Werkzeug
 flask-cors
-requests
+requests